Fourth Shinobi World War

The is an ongoing conflict between the Allied Shinobi Forces and Akatsuki. The battle began on the 8th of October and has stretched to the 9th.

Preparations for War
Its beginning was declared by Tobi when the five Kage and the leader of the Land of Iron unanimously refused to surrender the Eight-Tails and the Nine-Tailed Demon Fox for his Eye of the Moon Plan. He then stated that he would use the seven tailed beasts already captured by the Akatsuki in combating the ninja world. After this the Fifth Kazekage, the Fifth Mizukage, the A|Fourth Raikage, the Third Tsuchikage, and General Mifune agreed to form a Shinobi Alliance, pooling all their resources against Tobi. Later the daimyō of the Five Great Shinobi Countries approved the coalition and the Fifth Hokage joined the alliance while Kabuto Yakushi formed an alliance with Tobi.

Both factions began by gathering their strength and collecting intelligence about the other side in preparation for the upcoming hostilities. Kisame gathered intelligence on Kumogakure's military strength and on Killer B while travelling with him everywhere hidden inside Samehada. Anko Mitarashi and her team tracks Kabuto Yakushi, which led them to Tobi's headquarters. Other Shinobi Alliance teams have fanned out to collect other information about Akatsuki and their hideouts.

At the start, Kabuto had formed an alliance with Tobi, demonstrating his use of the Summoning: Impure World Reincarnation technique and increasing the forces of Akatsuki with the reincarnation of deceased members of the organisation. The Five Kage had also decided to hide the two remaining jinchūriki, Naruto and Killer B on an island in the Land of Lightning. Hiding Killer B and Naruto had the unintended result of allowing Naruto to learn to control the Nine-Tails chakra, much like the way Killer B has of the Eight-Tails (in the anime, however, Tsunade had intended for Naruto to train with B from the beginning). Having been successful in his training, Naruto has exhibited increased speed and strength when utilising the controlled chakra of the Nine-Tails but lacks the same finesse that Killer B had exhibited in utilising the Eight-Tails', crashing into the wall and crushing rocks whenever he uses the Nine-Tails chakra.

Despite being captured in the end and committing suicide to keep the information he held secret, Kisame was able to finish Akatsuki's preparations for the War by sending a summon shark with a scroll to his comrades, divulging the proximate location of the Turtle Island. With the battle between the two forces seeming to be on the horizon, Tobi dispatched Kabuto to retrieve the Nine-Tails and Eight-Tails with the reincarnated Deidara, but was stopped by Ōnoki, Akatsuchi and Kurotsuchi who were going to reinforce the forces on the Island Turtle. Kabuto escaped with Yamato, further adding to the intelligence sources that Akatsuki has on the Shinobi Alliance and also strengthening the White Zetsu Army clones with Yamato's powers.

Both the Allied Shinobi Forces and Akatsuki have amassed considerable forces for this war; 80,000 shinobi and samurai total make up the Alliance versus 100,000 Zetsu clones and reincarnated shinobi supplied by Kabuto making up Tobi's army.

Allied Shinobi Forces
The Allied Shinobi Forces created by the Five Great Nations and the Samurai of the Land of Iron consists of five main divisions, with Gaara of the Sand as the Regimental Commander. The 1st Division consists of mid-range fighters and is led by Darui. The Second Division is made up of close-range fighters and is led by Kitsuchi. The 3rd Division is under the command of Kakashi Hatake, and features both close- and mid-range fighters. The 4th Division contains only long-range fighters under the control of Gaara. Shikamaru is Gaara's right hand man and proxy commander of the Fourth Division as well. Finally, the 5th division was created for the purpose of special operations, and features ninjas with unique skills. Mifune is the leader of these special operatives. There are also four special divisions formed for the war. The Logistical Support and Medical Division led by Shizune comprises of medical ninja, the Surprise Attack Division led by Kankurō, has the task to ambush the enemy forces. The third is the Sensor Division with Ao as captain, and finally the Intelligence Division headed by Inoichi Yamanaka is intended to gather information and relay it to Gaara for strategy's sake.

Akatsuki
Akatsuki is composed of Tobi and Zetsu. Their primary fighting force is composed of 100,000 Zetsu clones created through a combination of the tailed beasts' chakra and Hashirama Senju's power. Tobi plans to use Sasuke Uchiha once he has recovered from his Mangekyō Sharingan transplant. Kabuto Yakushi has also joined forces with Akatsuki, reincarnating a large number of once-famous and powerful shinobi to supplement the White Zetsu Army.

Initial Deployment
Analysing their own and their enemy's location, the Allied Shinobi Forces have decided that Akatsuki will send a small fraction of their army by sea from the Mountains' Graveyard (Akatsuki's hideout) to Kumogakure, and that most of the army will travel by land. This would require the army to move through both the Land of Frost and the Land of Hot Water. An immediate evacuation notice was sent to both countries, and they will most likely evacuate to the south, in the Land of Fire. The First Division, which is the mid-range battle division, is stationed in the northern part of the Land of Lightning, in order to prevent the Akatsuki from using the small gulf to infiltrate the area from Mountain's Graveyard. The Second Division, or short-range battle division, is on the border of the Land of Lightning and the Land of Frost, sealing a northerly path into the Land of Lightning. The Third Division, or the short- to mid-range battle division, was advancing fast through the middle of the Land of Frost, but was called into the northern part of the Land of Hot Water to aid the Surprise Attack Division. The Fourth Division, the long-range battle division, is on the border of the Land of Lightning and the Land of Frost, sealing a southerly path into the Land of Lightning. Mifune's Fifth Division, the special battle division, is aligned in a large arc from the north part of the Land of Frost, through the middle of the border between the Land of Frost and the Land of Lightning, all the way to just south of the First Division, in order to aid any of the divisions that need immediate response, and to finish the seal on the Land of Frost and the Land of Lightning's border.

Secondary Deployment
As the confrontation develops, resulting in both the First and Fourth Divisions opposing two separate yet equally significant contingents of the enemy's forces, Shikaku Nara devises a strategy to better reflect the conflict's current developments. Confronted with two distinct groups, the decision is made not to individualise the targets and instead concentrate entirely on those facing Darui's First Division, by connecting their forces with those stationed within the Easterly end of Mifune's Fifth Division. The majority of Kitsuchi's Second Division will move simultaneously to this, proceeding along the ocean and sandwiching the enemy force in a pincer-manoeuvre, while the remainder attends to the adversaries that they are already battling.

Consequently, this will severely thin out the Second Division but as the Fifth Division fills in the gaps left behind by the Second Division, it will match that of the Fifth Division's formation, which then provides a solitary yet solid line of defence. As this occurs, Gaara's Fourth Division will make a slow retreat while moving into a sideways chevron formation, luring the enemy into following them. Eventually the top portion of this 'line' will break away and join the First Division, giving them yet further support.

Once the first targeted group of enemies is defeated, the joint forces of the First and supporting Fourth Division will switch to the remaining opposition at Gaara's Fourth Division, approaching from behind and decimating them in a single decisive strike. However; this preliminary plan relies upon the swift mobilisation of the Second and Fifth Divisions, so as to best employ Kitsuchi's units experience in combating the current enemy, and the belief that the opposition will be unable to mount a full attack upon the retreating long-range battle division, due partially to the enemy's suspicion over why the Fourth Division would split and their inability to get in close.

Night-time Deployment
As darkness falls and the remainder of the troops reallocate their forces in favour of observation, the Alliance takes the opportunity to centralise the Logistical Support and Medical Division behind their defences to attend to all the wounded shinobi. The compound is guarded by two Akimichi clan members at its only entrance and the chakra of anyone entering the compound is verified and cross referenced with the Alliance's headquarters, to prevent the infiltration of hostile intruders.

However, in spite of these various precautions, the Alliance's considerable defences fail to thwart the intrusion of a significant quantity of disguised White Zetsu Army clones and the resultant fatalities caused by the opposition's subsequent movements. As chaos ensues with individuals unable to ascertain friend from foe due to the chakra mimicking properties of the aforementioned clones, Shikaku Nara is tasked with the creation of a solution to counter this sudden perilous development. Despite much thought, he concludes that only Naruto's recently awakened capability to discern a person's "evil" intent, presents a viable resolution and due to his Shadow Clone Technique, many of the issues occurring within the dispersed divisions are solved simultaneously. This decision prompts the mobilisation of both jinchūriki in preparation for the following day.

Day One Deployment
Much less was initially known about the Akatsuki strategy, but it was made evident that their primary objective remained the acquisition of the surviving jinchūriki. From the small amount of information that had been divulged; Kabuto would maintain direct manipulation of the movements of the reincarnated individuals until they had reached their appointed destinations, with the intention of eradicating their personalities when the actual conflict began to turn them into mindless implements of death, while still manipulating any emotional response they could potentially illicit to full advantage, in the hopes of inflicting further damage. During the course of this approach, a small Surprise Attack and Diversion Platoon (comprised of Sasori, Deidara, Chūkichi and Shin) would attack from the air, utilising bombs and traps to disperse the enemy. However, realising that the movement of their entire army in such a large and apparent fashion would be far too conspicuous, the decision was instead undertaken to dislocate the 100,000 White Zetsu Army clones beneath the ground, in order to thoroughly conceal the approach of the main contingent of their forces. Though a large amount of these clones were eventually unearthed, thousands more were able to proceed unobstructed underground to their respective battlegrounds, due in part to the diversionary tactics made possible by the addition of Kabuto's reincarnated shinobi.

Concurrent to the developing conflict, Black Zetsu would utilise the resulting turmoil in order to infiltrate the daimyō's safe house as per Tobi's orders, with the sole intention of using these valued captives as bargaining chips to draw out the jinchūriki. However, with the jinchūriki's decision to expose themselves and take direct action before this assignments completion, it was deemed unnecessary and so Black Zetsu's role was altered to instead engage with the daimyō's guards, ensuring their continued separation from the remainder of the Allied Shinobi Forces.

Night-time Deployment
As the confrontation progresses and night falls upon the first day, Tobi's true intentions and the reasons behind his confidence in his original strategy, which didn't account for Kabuto's inclusion or contributions, is revealed. The two opposing sides would effectively be forced into a staring contest as the Allied Shinobi Forces focus on tightening defences and tending to the wounded or resting. Tobi, aware that this would make the Allied Shinobi completely reliant upon their sensor shinobi in order to remain vigilant, then begins taking this advantage of this by utilising the Zetsu clones' Substitute Technique in conjunction with the chakra obtained from members of the Allied Shinobi Forces during the previous battles. By covertly placing these transformed Zetsu among the injured and scattered troops of the Allied Shinobi, they could then proceed to assassinate any isolated individuals while remaining undetected. This results in causing chaos and disagreement within the ranks of the Allied Shinobi who begin to suspect one another of committing these deeds without any definitive proof, but while also minimising the causalities suffered by the Akatsuki forces in the process. In addition, the attack of the transformed Zetsu also aimed to force the shinobi alliance to counter these insurgents, placing Naruto in the battlefield whose ability to recognise "evil" intent Tobi has learned from the intel gathered by Kisame.

Unbeknownst to the opposition, Tobi had also begun developing further contingencies in preparation for the second day of the conflict, creating his own Six Paths of Pain by utilising the former jinchūriki and customising them with both a Rinnegan and a Sharingan.

Battle at Mountains' Graveyard

 * Location: Mountains' Graveyard
 * Combatants
 * Akatsuki: Kabuto Yakushi, Surprise Attack and Diversion Platoon
 * Allied Shinobi Forces: Infiltration and Reconnaissance Party
 * Duration
 * Manga: Chapter #516 to #517
 * Anime: Naruto: Shippūden #261 to #262
 * Outcome: Infiltration and Reconnaissance Party are all captured. Muta Aburame manages to send intel back to HQ. Akatsuki tactical victory. Allied Shinobi Forces strategic victory.

When Akatsuki starts mobilising from the Mountains' Graveyard, Anko Mitarashi orders the rest of the Infiltration and Reconnaissance Party to inform the rest of the Allies while she continues to investigate. She is found and defeated by Kabuto Yakushi. Akatsuki's Surprise Attack and Diversion Platoon pursues and ultimately captures the remaining members of the Reconnaissance Party, but cannot stop them from getting word to the Alliance's HQ.

Battle of the Surprise Attack Divisions

 * Location: Land of Hot Water
 * Combatants
 * Akatsuki: Surprise Attack and Diversion Platoon
 * Allied Shinobi Forces: Surprise Attack Division
 * Duration
 * Manga: Chapter #517 to #519
 * Anime: Naruto: Shippūden #262 to #263
 * Outcome: Deidara is captured. Shin and Sasori return to the afterlife. Chūkichi flees. Muta Aburame is killed. Allied Shinobi Forces victory.

The Alliance sends its Surprise Attack Division to ambush Akatsuki's forces in the Land of Hot Water. Akatsuki sends its Surprise Attack and Diversion Platoon to do the same. The two are drawn into conflict. The Allies eventually emerge victorious - Sasori and Shin are released from the Impure World Reincarnation and Deidara is captured - and they are even able to rescue some of the captured members of the Infiltration and Reconnaissance Party.

Allied Force's Ambush

 * Location: Land of Hot Water
 * Combatants
 * Akatsuki: Haku, Pakura, Gari, the previous Seven Ninja Swordsmen of the Mist, portion of the White Zetsu Army, Chen (Anime Only)
 * Allied Shinobi Forces: Part of the Surprise Attack Division, Third Division, Naruto Uzumaki's shadow clone
 * Duration
 * Manga: Chapter #520 to #573
 * Anime: Naruto: Shippūden #265 to #330
 * Outcome: Tajiki and dozens of Allied Shinobi killed or wounded. All reincarnated shinobi sealed or released. Allied Shinobi Forces victory.

Following the success of their first mission, part of the Surprise Attack Division is sent to ambush another Akatsuki cell. They encounter a group consisting of Zabuza Momochi, Haku, Pakura, Gari and, though outnumbered, attack. When the attack fails, the Third Division is called in to assist. Akatsuki's forces - reinforced with reincarnated members of the Seven Ninja Swordsmen of the Mist (and Chen in the anime) - cause heavy casualties amongst the Third Division. Zabuza and Haku are successfully sealed early on, but sealing of the others proves more challenging. By the second day of the war three reincarnated shinobi remain, now bolstered by White Zetsu. The assistance of one of Naruto Uzumaki's shadow clones enables the Third Division to deal with the remaining Akatsuki forces.

Battle in the Land of Frost

 * Location: Border of the Land of Frost and the Land of Lightning
 * Combatants
 * Akatsuki: Around 20,000 clones of the White Zetsu Army
 * Allied Shinobi Forces: Second Division, westerly section of the Fifth Division, Naruto Uzumaki's shadow clone
 * Duration
 * Manga: Chapter #521 to #573
 * Anime: Naruto: Shippūden #264 to #330
 * Outcome: Tactical withdrawal of the Allied Shinobi Forces to aid the First Division. Eventual Allied Shinobi Forces victory.

When the war begins, the Second Division is deployed to the border of the Land of Frost and the Land of Lightning. Approximately 20,000 White Zetsu are detected moving into the Land of Lightning underground, prompting Kitsuchi and Kurotsuchi to use Earth Release: Opening Earth Rising Excavation to unearth them. In an opening salvo the Second Division is able to destroy scores of White Zetsu, but it quickly descends into one of attrition, tiring much of the Second Division and allowing many White Zetsu to escape. Most of the Second Division is sent in pursuit of these Zetsu by assisting the First Division, leaving their remaining forces to face a new threat: White Zetsu that have infiltrated the Alliance. Members of the Second Division are slowly eliminated by the Zetsu and left uncertain about who to trust until the second day when the arrival of one of Naruto Uzumaki's shadow clones allows them to root out all of the Zetsu.

First Battle on the Land of Lightning's Coast

 * Location: North-western coast of the Land of Lightning
 * Combatants
 * Akatsuki: Thousands of the White Zetsu Army, Asuma Sarutobi, Hizashi Hyūga, Dan Katō, Kakuzu, Kinkaku, Ginkaku
 * Allied Shinobi Forces: First Division, parts of the Second Division, Fourth Division, the eastern tail of the Fifth Division
 * Duration
 * Manga: Chapter #525 to #536
 * Anime: Naruto: Shippūden #268 to #276
 * Outcome: Atsui, Samui, and Ginkaku are sealed within the Benihisago. Kinkaku is sealed within the Kohaku no Jōhei. Asuma Sarutobi is sealed. All White Zetsu are killed. Several shinobi are killed. Dan Katō is trapped within the Four Violet Flames Formation. Kakuzu and Hizashi Hyūga are subdued by Chōji Akimichi. Allied Shinobi Forces victory.

When the war begins, the First Division is stationed along the north-western coast of the Land of Lightning. They are soon confronted by the reincarnated shinobi and White Zetsu that escaped the Second Division's defense along the country's perimeter. The two sides engage each other, with Division Commander Darui facing off with the Gold and Silver Brothers. Darui initially struggles with the brothers and their Treasured Tools of the Sage of the Six Paths, but eventually is able to turn the tools against the brothers to capture Ginkaku in their own Benihisago. This enrages Kinkaku to the point that he enters a version 2 form, which he uses to tear through the First Division. After reinforcements from the Second, Fourth, and Fifth arrive and the Alliance HQ sends the Kohaku no Jōhei to the battlefield, Kinaku is captured.

With the Gold and Silver Brothers dealt with, the Allies turn their attention to the remaining reincarnated ninja: Asuma Sarutobi is defeated by his former students; Kakuzu and Hizashi Hyūga are sealed with the help of Chōji Akimichi; Dan Katō is trapped within a Four Violet Flames Formation. The remaining White Zetsu are seemingly defeated, leaving the Allies victorious.

Battle in the Land of Hot Water

 * Location: Land of Hot Water
 * Combatants
 * Akatsuki: Hanzō, Chiyo, Kimimaro, Chūkichi, Ibuse
 * Allied Shinobi Forces: Part of the Surprise Attack Division, Mifune, samurai and shinobi of the Fifth Division, Naruto Uzumaki's shadow clone
 * Duration
 * Manga: Chapter #530 to Chapter #591
 * Anime: Naruto: Shippūden #272 to #340
 * Outcome: Ibuse killed. Several samurai killed. All reincarnated shinobi released from Impure World Reincarnation. Kankurō's portion of the Surprise Attack Division paralysed, but later given antidote. Allied Shinobi's victory.

While part of the Surprise Attack Division is transporting the captured Deidara they are met by a restaffed Surprise Attack and Diversion Platoon. The Surprise Attack Division attempts to escape, but is paralysed by Hanzō's summoned Ibuse. They are rescued by samurai of the Fifth Division, with Mifune engaging and ultimately emerging victorious over Hanzō. Kimimaro and Chiyo prove more elusive, and it is not until the Impure World Resurrection is released on the second day that they are defeated.

Second Battle on the Land of Lightning Coast

 * Location: North-western coast of the Land of Lightning
 * Combatants
 * Akatsuki: Tobi, the Demonic Statue of the Outer Path
 * Allied Shinobi Forces: First Division, parts of the Second Division, Fourth Division, the eastern tail of the Fifth Division
 * Duration
 * Manga: Chapter #536 to #537
 * Anime: Naruto: Shippūden #276
 * Outcome: Dan Katō is freed. Kakuzu escapes from being sealed. Hundreds of Allied Shinobi dead in Demonic Statue of the Outer Path's rampage. Tobi retrieves the Benihisago and Kohaku no Jōhei for containing the Gold and Silver Brothers. Akatsuki victory.

Almost immediately after the the First Division and its backup defeats the last of Akatsuki's forces, Tobi appears on the battlefield and summons the Demonic Statue of the Outer Path. Despite the efforts of Kitsuchi, Chōza, and Chōji, the Statue decimates the Allied forces. While taking shelter from the Statue's attacks, members of the First Division begin to realise the attack is just a distraction while Tobi acquires the captured Gold and Silver Brothers. They aren't able to stop him in time and he escapes with the Benihisago and Kohaku no Jōhei. His mission accomplished, Tobi de-summons the statue.

The Battle for the Daimyō's Protection

 * Location: Unknown
 * Combatants
 * Akatsuki: Black Zetsu
 * Allied Shinobi Forces: Daimyō Protection Squad, Naruto Uzumaki's shadow clone
 * Duration
 * Manga: Chapter #536 to #562
 * Anime: Naruto: Shippūden #276 to #322
 * Outcome: Black Zetsu is incapacitated. Allied Shinobi Forces victory.

In order to force the Allies' cooperation, Black Zetsu is sent to capture the daimyō of the Five Great Shinobi Countries. He is found and stopped by the Daimyō Protection Squad almost immediately after he arrives at the secret compound. Before he begins fighting he senses Naruto Uzumaki's appearance on the battlefield and informs Tobi of this development. The daimyō's capture ceases to matter, but Black Zetsu is instructed to keep the Daimyō Protection Squad busy. One of Naruto's shadow clones arrives on the second day to help capture Black Zetsu.

Night One
At the end of the first day of the battle, both the Alliance and Akatsuki received massive casualties, having effectively halved both their battle forces. The 80,000 strong Allied Shinobi Forces were brought down to 40,000, and the 100,000 strong White Zetsu Army was brought down to 50,000, on top of the several already sealed reincarnated shinobi.

During the day of fighting, members of the White Zetsu Army infiltrated the Alliance's ranks. Once night falls, the disguised Zetsu begin methodically eliminating key Allied personnel all across the battlefield. The Alliance is thrown into disarray until Sakura Haruno is able to determine what is happening. Despite this, there are no effective countermeasures against the Zetsu and vigilance is unable to prevent additional deaths. Suspicion reigns over the Allies.

Skirmishes in the Land of Lightning

 * Location: Land of Lightning
 * Combatants
 * Akatsuki: Platoon of White Zetsu Army posing as Allied Shinobi, Toroi
 * Allied Shinobi Forces: Naruto Uzumaki, Killer B, Gamahiro, Musai, Nonota
 * Duration
 * Manga: Chapter #545 to Chapter #546
 * Anime: Naruto: Shippūden #296
 * Outcome: All White Zetsu killed. Naruto uses his Shadow Clone Technique to disperse clones into the battlefield. Toroi is sealed. Allied Shinobi Forces victory.

Early in the night, Naruto and Killer B escape their confinement in the Land of Lightning. Although the Fourth Raikage and Fifth Hokage are sent to intercept them and place them under guard again, Naruto is able to convince them to allow him and B to fight.

Naruto and B's contributions immediately prove invaluable. They encounter a platoon of Allied shinobi heading towards HQ, which Naruto recognizes as disguised Zetsu. Naruto and B defeat them all and Naruto sends his shadow clones to various battlefields to lend whatever assistance they can. As Naruto and B continue outbound from the Land of Lightning, they are able to save Musai and Nonota from a reincarnated Toroi.

First Southern Battle in the Land of Lightning

 * Location: Land of Lightning
 * Combatants
 * Akatsuki: Mū, Second Mizukage, Third Raikage, Fourth Kazekage, Giant Clam
 * Allied Shinobi Forces: Part of the Fourth Division with its Commander Gaara, Ōnoki, Naruto Uzumaki's shadow clone
 * Duration
 * Manga: Chapter #546 to #558
 * Anime: Naruto: Shippūden #296 to #302
 * Outcome: Dozens of Allied Forces shinobi are killed. The Third Raikage, Second Mizukage, Fourth Kazekage, and half of Mū are sealed. Allied Shinobi Forces victory.

The Fourth Division encounters the reincarnated Mū on the first day of hostilities. Akastuki responds by sending the Second Mizukage, the Third Raikage, and the Fourth Kazekage to reinforce Mū. The Alliance likewise sends Ōnoki to assist the Fourth Division. Despite this, the Fourth Division avoids conflict until the second day when other Divisions - their own battles won - can be called in to help.

Gaara launches the first attack - which in turn is countered by the Fourth Kazekage's gold dust - Ōnoki engages Mū, and elements of the First Division attack the Raikage and Mizukage from the rear. The Fourth Kazekage is captured and sealed while protecting the Raikage and Mizukage, but the remaining Kage are more elusive: the Raikage is largely impervious to damage, the Mizukage and his summoned clam cannot be located in their mirage, and Ōnoki is unable to overpower Mū.

When Naruto's shadow clone arrives it takes Mū by surprised and, in the ensuing confusion, Mū is sealed before he can respond. Naruto next focuses on the Third Raikage, whose defenses are impenetrable and whose attacks are unstoppable. When his and the Alliance's combined efforts can do nothing against the Raikage, Naruto maneuvers the Raikage against himself, using his own attacks to break his own defenses and creating an opening to seal him. Meanwhile, Gaara and Ōnoki face-off with the Mizukage. They're able to destroy the Mizukage's clam, but struggle with his Steaming Danger Tyranny. Gaara is ultimately able to sneak some of the Fourth Kazzekage's remaining gold dust into the Mizukage's technique, neutralizing it and allowing the Mizukage to be sealed.

Battle Against the Dōjutsu Duo

 * Location: Land of Lightning
 * Combatants
 * Akatsuki: Itachi Uchiha (beginning), Nagato, Giant Drill-Beaked Bird, Giant Multi-Headed Dog, Giant Snake-Tailed Chameleon
 * Allied Shinobi Forces: Naruto Uzumaki, Killer B, Itachi Uchiha (later)
 * Duration
 * Manga: Chapter #548 to #552
 * Anime: Naruto: Shippūden #298 to #299
 * Outcome: Itachi is freed from Kabuto's control. Nagato is sealed. Allied Shinobi Forces victory

Kabuto Yakushi decides to temporarily kill Naruto and Killer B in order to deal with them in the short term and make it easier to use them against Tobi in the long term. To that end, he sends the reincarnated Nagato and Itachi Uchiha after them. While Nagato attacks them with different summons, Itachi activates the Kotoamatsukami he planted on Naruto before his death, releasing him from Kabuto's control and allowing him to assist with defeating Nagato. Though his body was frail, Nagato is able to regain his mobility by absorbing B's version 2 chakra. Although this revitalized Nagato is nearly able to remove Naruto's soul, he is overpowered by the three and sealed by Itachi's Susanoo.

Battle Against the Sound Four

 * Location: North-western coast of the Land of Lightning and Land of Frost
 * Combatants
 * Akatsuki: The Sound Four
 * Allied Shinobi Forces: Shikamaru Nara, Chōji Akimichi, Neji Hyūga, Kiba Inuzuka, Naruto Uzumaki's shadow clone
 * Duration
 * Anime:  Naruto: Shippūden  #302 to #304
 * Outcome: Reincarnated Sound Four souls released. Allied Shinobi Forces victory.

On various battlefields, the reincarnated Sound Four tries to take revenge against the members of the Sasuke Retrieval Team that killed them years earlier. Individually the Sound Four are defeated, but with the Space–Time Technique Formula: Underworld Turnover their defeated bodies ensnare the souls of their targets. The vengeance that fuels their technique is traceable by Naruto's shadow clone, who locates them, returns their souls to the afterlife, and frees their victims.

Hunt for Hayate

 * Location: Logistical Support and Medical Division forest
 * Combatants
 *  Akatsuki: Hayate Gekkō, two unidentified reincarnated shinobi
 * Allied Shinobi Forces: Iō, Yokaze, Yūgao Uzuki, Sakura Haruno
 * Duration
 * Anime: Naruto: Shippūden #307 to #308
 * Outcome: Hayate Gekkō and two unidentified shinobi are sealed. Allied Shinobi Forces victory.

The Logistical Support and Medical Division prioritizes the protection of the corpses of those with kekkei genkai so that Akatsuki cannot use their bodies against the Alliance. A reincarnated Hayate Gekkō is sent to steal a scroll the bodies are stored in. He succeeds, but is pursued by Yūgao Uzuki, his former lover. Yūgao is initially unwilling to fight Hayate, forcing Sakura Haruno to deal with him. Yūgao does finally intervene when Hayate is about to kill Sakura and her presence stays his blade long enough for a Sealing Team to capture him.

Battle Against Tatewaki

 * Location: Land of Lightning forest
 * Combatants:
 * Akatsuki: Tatewaki
 * Allied Shinobi Forces: Karui, part of the Second Division, Naruto Uzumaki's shadow clone
 * Duration
 * Anime: Naruto: Shippūden #309 to #310
 * Outcome: Tatewaki able to break contract with Kabuto Yakushi and return to the afterlife. Allied Shinobi Forces victory.

In the anime, part of the Second Division is attacked by a reincarnated Tatewaki, who they struggle to fight against. A short time later, one of Naruto's shadow clones arrives to help. Having met Tatewaki when he was alive, Naruto is able to speak of him and informs him of the fates of Shū and Chiyo. When he hears they are safe and happy, Tatewaki's soul is put at peace and he is released from the Impure World Reincarnation.

Battle Against Yota

 * Location: North-western coast of Land of Lightning and Land of Frost and Logistical Support and Medical Division
 * Combatants:
 * Akatsuki: Yota, three White Zetsu clones taking on his appearance, portion of the White Zetsu Army
 * Allied Shinobi forces: portion of the Second Division, Fourth Division, Shikamaru Nara, Chōji Akimichi, Ino Yamanaka, Kiba Inuzuka, Naruto Uzumaki's shadow clone
 * Duration
 * Anime: Naruto: Shippūden #313 to #315
 * Outcome: Yota able to break contract with Kabuto Yakushi and return to the afterlife. Allied Shinobi Forces victory.

A reincarnated person appears on three different battlefields and produces strange weather patterns. Members of Konoha's Rookie Nine recognize him as Yota, who they knew when they were in the Academy. However, only one of the three can be the real Yota, the other two being transformed Zetsu. One of Naruto's shadow clones locates the real Yota and reminisces with him about the fun they had when they were kids. Yota's soul is put at peace and he is released from the Impure World Reincarnation, but not before he destroys his corpse to prevent being revived again.

Battle Against the Lesser Reincarnated Shinobi

 * Location: Land of Lightning
 * Combatants:
 * Akatsuki: Torune, Heiji, Chūkaku, Daimaru, Osoi, many lesser reincarnated shinobi, White Zetsu clones
 * Allied Shinobi forces: Part of the Fourth Division, including Temari, Yukata, Matsuri, Musai, Nonota, Shino Aburame, Naruto Uzumaki's shadow clone
 * Duration
 * Anime: Naruto: Shippuden #316 to #317
 * Outcome: All reanimated shinobi sealed. Allied Shinobi Forces victory.

The loss of so many valuable pawns forces Kabuto to use the ninja he mistakenly reincarnated in pursuit of other, stronger ninja. He places Torune in charge of a squad with the mission to release some of the shinobi sealed by the Allies, such as Toroi and the Third Raikage. All but Torune are caught in traps placed by the Fourth Division around the sealed ninja. Torune attempts to use a kinjutsu that would devastate the Allied shinobi, but is stopped and sealed by Shino Aburame and one of Naruto's shadow clones.

Battle Against Fukai

 * Location Land of Lightning
 * Combatants:
 * Akatsuki: Fukai, portion of the White Zetsu Army
 * Allied Shinobi forces: Killer B, Motoi
 * Duration
 * Anime: Naruto: Shippuden #318
 * Outcome: All White Zetsu Army clones defeated and Fukai able to break contract with Kabuto Yakushi and return to the afterlife. Allied Shinobi Forces victory.

Kabuto decides to test Killer B's skills by reincarnating his predecessor as the Eight-Tails' jinchūriki: Fukai. B, with Motoi's help, engages Fukai, but they are soon put on the defensive. Motoi is nearly killed trying to buy time for B to escape, but B comes back to save him. B speaks with Fukai telepathically and vows to help him however he can. Glad that B has found the kind of purpose he lacked in his own life, Fukai's soul is put at peace and he is released from the Impure World Reincarnation.

Water Attack Raid Unit Rescue

 * Location Seventh Front
 *  Combatants:
 *  Akatsuki: Two thousand White Zetsu Army clones
 * Allied Shinobi Forces: Water Attack Raid Unit, Thundercloud Unit, Omoi, Naruto Uzumaki's shadow clone
 * Duration
 * Anime: Naruto: Shippuden #320
 * Outcome: All White Zetsu Army clones defeated. Allied Shinobi Forces victory.

In the anime, the Water Attack Raid Unit comes under attack near the Seventh Front by the White Zetsu Army. Allied Shinobi HQ sends the Thundercloud Unit as reinforcements, who soon find themselves getting overwhelmed as well. Omoi abandons his post to assist them, but by the time he arrives the Water Attack Raid Unit has already been defeated. Eventually, Omoi locates the Thundercloud Unit and with their help is able to eventually defeat the white Zetsu.

Second Southern Battle in the Land of Lightning

 * Location: Land of Lightning
 * Combatants
 * Akatsuki: Madara Uchiha, Mū's other half
 * Allied Shinobi Forces: Fourth Division, Naruto Uzumaki's shadow clone, the five Kage, the Hokage Guard Platoon,
 * Duration
 * Manga: Chapter #559 to #600
 * Anime: Naruto: Shippūden #321 to #343
 * Outcome: Heavy Allied Shinobi casualties. All Kage critically wounded. Mū released from the Impure World Reincarnation. Madara severed contract with technique and rendezvous with Tobi. Akatsuki victory.

When he was attacked by Naruto's shadow clone earlier, Mū's body instinctively split in two, of which only one was sealed. The second half cannot release the first half, so Kabuto uses the only option he has left: he uses Mū as a medium to summon a reincarnated Madara Uchiha. Kabuto encourages Madara to show what made him so legendary, which Madara obliges by attacking the nearby Fourth Division. Gaara, Ōnoki, Naruto's shadow clone, and the rest of the Allies present are already outmatched by Madara, which is only made worse when Madara drops two meteorites upon them, wiping out most of the Fourth Division. Madara attacks the survivors with Wood Release Secret Technique: Nativity of a World of Trees, which Naruto does his best to defend against.

Naruto's shadow clone is beginning to run low on chakra and cannot hold out against Madara for much longer. The three remaining Kage (A, Tsunade, and Mei Terumī) arrive on the battlefield to join Gaara and Ōnoki against Madara, instructing Naruto to trust the fight to them. Naruto's clone vanishes, remnants of the Fourth Division pursue Mū's half, and the Kage engage Madara. Although the Kage pull off some attacks that impress even Madara, they cannot hope to defeat him so long as he is an immortal reincarnation that recovers from all injuries. All they can hope to do is endure against Madara's various powers until Kabuto is defeated and the Impure World Reincarnation is broken.

As night starts to fall, the Kage cannot last much longer, Madara having multiple clones that are each using Susanoo to outnumber them five-to-one. Before he can wage a final attack, Madara is engulfed in light and his soul begins to ascend, Kabuto having elsewhere been defeated. Madara releases himself from the influence of the Impure World Reincarnation, granting him an immortal body. Free to do what he wants, Madara decides to go find Naruto. The Kage try to stop him, but each is brought to the verge of death in an unseen battle and Madara escapes.

First Battle Against the Eye of the Moon Plan

 * Location: Land of Lightning, Kamui's dimension
 * Combatants
 * Akatsuki: Tobi, the six reincarnated jinchūriki, six of the sealed Tailed Beasts, Demonic Statue of the Outer Path, Madara Uchiha
 * Allied Shinobi Forces: Naruto Uzumaki, Killer B, Kakashi Hatake, Might Guy
 * Duration
 * Manga: Chapter #563 to #609
 * Anime: Naruto: Shippūden #323 to #362
 * Outcome: The six tailed beasts are resealed in the Demonic Statue of the Outer Path. The six reincarnated jinchūriki are released from the Impure World Reincarnation. Ten-Tails is revived. Tactical Akatsuki victory.

Tobi uses the reincarnated bodies of the former jinchūriki to create his own Six Paths of Pain, each with their old tailed beasts sealed back into them. They converge on Killer B and the real Naruto and engage them in battle. After a brief exchange B is able to restrain and nearly seal all six, but they free themselves by entering version 2 forms. In the chaos created by these stronger opponents, Tobi almost captures Naruto, but he is stopped by the arrival of Kakashi Hatake and Might Guy.

Tobi begins to have some of the jinchūriki enter Tailed Beast Mode to overwhelm the Allied shinobi. The Four-Tails goes after and swallows Naruto, which gives its jinchūriki, Rōshi, a chance to communicate to Naruto how to release them from Tobi's control. Naruto escapes from the Four-Tails' mouth and locates the chakra receiver on its body. By removing it he frees Rōshi and the Four-Tails, to which Tobi responds by first reclaiming the Four-Tails and then by having all the other jinchūriki fully transform. The Nine-Tails is touched by Naruto's determination to help its fellow tailed beasts and thus gives its full cooperation to Naruto. Their new and improved Nine-Tails Chakra Mode allows them to defeat and free the other tailed beasts, but Tobi reclaims them into Demonic Statue of the Outer Path too.

Tobi fights Naruto, B, Kakashi, and Guy by himself until he is alerted to Kabuto's defeat. Running out of options, he initiates a premature revivial of the Ten-Tails by depositing the sealed Gold and Silver Brothers (who contain remnants of the Nine-Tail' chakra) and one of the Eight-Tails' tentacles into the Statue. He places a barrier around it as it undergoes its transformation and engages his four opponents in the meantime. Their efforts to attack Tobi fail until they notice a connection between his ability to become intangible and Kakashi's Kamui. By taking advantage of this connection, they are able to land a successful attack and destroy his mask, revealing him as Obito Uchiha.

Moments after his identity if exposed, Obito is joined by Madara, having just finished up with the five Kage. Noticing that the Statue has not had the Eight or Nine-Tails sealed into it yet, Madara attempts to take the beasts from Naruto and B before the Ten-Tails is revived. Kakashi and Guy defend them while Naruto and B try to destroy the Statue, but they're too late and the Ten-Tail is revived.

Battle Against the Impure World Reincarnation Technique

 * Location: Mountains' Graveyard
 * Combatants
 * Akatsuki: Kabuto Yakushi
 * Other: Itachi Uchiha, Sasuke Uchiha
 * Duration
 * Manga: Chapter #578 to #589
 * Anime: Naruto: Shippūden #333 to #339
 * Outcome: Kabuto is trapped in Izanami and unable to fight. All reincarnated shinobi (except Madara Uchiha) are released. Tactical Allied Shinobi Forces victory.

After freeing himself from Kabuto's control, Itachi tasks himself with breaking the Impure World Reincarnation. He traces Kabuto to the Mountains' Graveyard. Along the way Itachi is found and joined by his younger brother, Sasuke. They locate Kabuto, but know they cannot kill him if the Impure World Reincarnation is to be released. After taking precautions to protect himself from their genjutsu, Kabuto takes advantage of their unwillingness to kill him by bombarding them with all the abilities he's acquired for himself: the pilfered abilities of the late Sound Four, the research of Orochimaru, and a Sage Mode he's trained to perfection. The Uchiha brothers defend themselves, helped particularly by their Susanoo. Ultimately, Itachi traps Kabuto in the endless loop of Izanami. Defeated, Kabuto is compelled via genjutsu to release Impure World Reincarnation, sending Itachi and the other reincarnated shinobi back to the afterlife.

Battle Against the Ten-Tails

 * Location: Land of Lightning, Kamui's dimension
 * Combatants
 * Akatsuki: Obito Uchiha, Madara Uchiha, the Ten-Tails, Black Zetsu
 * Allied Shinobi Forces: Naruto Uzumaki, Killer B, Kakashi Hatake, Might Guy, all avaliable divisions of the Allied Forces, the four reincarnated Hokage, the five Kage
 * Independent: Taka, Orochimaru, the seven tailed beasts
 * Duration
 * Manga: Chapter #610 to #656
 * Anime: Naruto Shippūden #363 onward
 * Outcome: Allied Shinobi Forces' Headquarters destroyed. Allied Shinobi Forces suffer major casualties. Obito temporarily jinchūriki of Ten-Tails until they are released. Obito is forced to resurrect Madara by force. Allied Shinobi Forces tactical victory. Akatsuki strategic victory.

Though the Ten-Tails is restored, it will still be some time before the moon is in a position to complete the Eye of the Moon Plan. Madara and Obito therefore opt to eliminate the opposition in the meantime. They take control of the Ten-Tails and use it to try and destroy Naruto, B, Kakashi, and Guy, but the remaining Allied Shinobi Forces arrive in time to stop the attack. They combine their efforts to restrain and bind the Ten-Tails, but the victory is brief; the Ten-Tails transforms and frees itself.

Madara and Obito recognize the coordination involved to bring such a huge force together so effectively and use the Ten-Tails to destroy the Allied HQ to prevent future coordinating. All stationed there are killed, but Shikaku Nara is able to communicate one final attack plan to the Allies. Many ninja die as they move into position - including Neji Hyūga - but they are able to pull off Shikaku's final plan and sever the connection between the Ten-Tails and the Uchihas. Freed, the Ten-Tails prepares to use Tenpenchii. Kakashi attempts to send the beast away, but Obito intercepts him and warps them both to the other dimension. Tenpenchii levels the area but none are killed due to the protective cloak Naruto coats everyone with.

Before the Ten-Tails can launch another attack it is stopped by the arrived Hokage, reincarnated by Orochimaru at the direction of Sasuke. Hashirama Senju restrains the Ten-Tails and he and the other Hokage trap it in a barrier. Though it can't move, the Ten-Tails spawns miniature clones of itself to protect it. The Allies fight its copies but it becomes apparent that the Ten-Tails is on the verge of a final transformation. Naruto, Sasuke, and Sakura join forces against it, badly damaging it.

Meanwhile, in the other dimension, Kakashi and Obito spar. Being old comrades, Obito tries to convince Kakashi that his actions are right and that the world as it is must be eliminated. Kakashi refuses to agree and badly wounds Obito, forcing him to retreat back to the real world. When Madara senses Obito's return, Madara tries to take advantage of him in his weakened state to force Obito to restore him to life. Obito resists and instead seals the Ten-Tails into his body, becoming its jinchūriki. The Hokage, no longer preoccupied with restraining the Ten-Tails, attack it, only to discover Obito's new power cancels out the regenerative advantages of their reincarnated bodies. The Allies try various methods of damaging Obito, but only senjutsu has any kind of success.

With the moon nearly in position, Obito transforms into the Ten-Tails' final form: a giant tree capable of absorbing chakra from anyone it touches. With their numbers dwindling and time running out, the Allies prepare for one final assault. Naruto and Sasuke launch a a final attack while the remaining allies, rallied by their respective newly rejuvenated Kage, provide support. The tailed beasts the Ten-Tails is composed of are stripped from Obito and released, leaving him defeated and unable to move. Because Obito is no longer able to resist, Black Zetsu takes control of him and forces him to revive Madara.

Second Battle Against the Eye of the Moon Plan

 * Location: Land of Lightning, Kamui's Dimension
 * Combatants
 * Akatsuki: Madara Uchiha, Black Zetsu, White Zetsu clones, Demonic Statue of the Outer Path, Guruguru
 * Allied Shinobi Forces: All available divisions of the Allied Forces, the four reincarnated Hokage
 * Independent: Taka, Orochimaru, the seven tailed beasts, Obito Uchiha, Kabuto Yakushi
 * Duration
 * Manga: Chapter #657 to #677
 * Outcome: The nine tailed beasts (except Kurama's Yin half) are resealed within the Demonic Statue of the Outer Path. Madara becomes the Ten-Tails' jinchūriki. Yin-Kurama and parts of Shukaku and Gyūki are sealed into Naruto. Madara activates the Infinite Tsukuyomi. Akatsuki victory.

Though living again, Madara is left unable to see, having forfeited his eyes shortly before his original death. Until he can reacquire them he immobilizes Hashirama and absorbs his senjutsu chakra to allow him to sense things around him. His first order of business is capturing the tailed beasts again. He is initially no match for the nine beasts until a white Zetsu delivers one of his Rinnegan to him. He uses it to summon the Demonic Statue of the Outer Path from Obito's body and then quickly seals all the tailed beasts, including B's Eight-Tails and Naruto's Nine-Tails, into it, triggering another rebirth of the Ten-Tails. Sasuke tries to stop him, so Madara stabs him with his own sword.

Meanwhile, Guruguru keeps the Allied Shinobi Forces occupied with Sage Art: Wood Release: True Several Thousand Hands to battle them. Naruto, dying from the removal of the Nine-Tails, is delivered to the reincarnated Minato Namikaze by Gaara so that the half of the Nine-Tails' chakra that Minato has can be sealed into him. Black Zetsu intercepts the transfer and takes the Nine-Tails' chakra for itself, but this creates an opening for Obito to reclaim control of his body. Obito, having finally decided he was wrong, escapes to the other dimension with Naruto and Sakura (who is providing emergency life support), where he begins sealing the Nine-Tails' chakra from Black Zetsu to Naruto. Elsewhere, a dying Sasuke is approached by Kabuto, who also had a change of heart, and he begins healing Sasuke's wounds.

Madara, now the Ten-Tails' jinchūriki, is left to deal with the stragglers. With nobody else who can perform senjutsu around, taijutsu is the only means of combating him. Might Guy decides that this is a worthy cause for him and decides to give his life to defeat Madara. He opens all Eight Gates and assaults Madara with his Evening Elephant. This takes a heavy toll on his body but doesn't stop Madara, forcing him to resort to his final attack: Night Guy. This time Madara is badly injured, but still he survives. Spent, the life fades from Guy.

While on the border between life and death, Naruto and Sasuke each meet with the Sage of the Six Paths, who offers them a portion of his power to defeat the Ten-Tails at long last. Once each is restored to health, Naruto saves Guy from death and they engage Madara with their new powers: Sasuke's Rinnegan and Naruto's simultaneous access to all of the nine tailed beasts' abilities. No match for Naruto and Sasuke, Madara becomes determined to reacquire his remaining Rinngean. He steals Kakashi's Sharingan and uses it follow Obito to the other dimension where he takes the Rinnegan Obito has been using. Restored to full power, Madara returns to the real world and initiates the Infinite Tsukuyomi.

Battle Against the Infinite Tsukuyomi

 * Location: Land of Lightning, Kaguya's Dimension
 * Combatants
 * Akatsuki: Madara Uchiha
 * Allied Shinobi Forces: Naruto Uzumaki, Sakura Haruno, Kakashi Hatake, the four reincarnated Hokage, the spirit of other deceased Kages
 * Independent: Sasuke Uchiha, Obito Uchiha, Black Zetsu, Kaguya Ōtsutsuki, Hagoromo Ōtsutsuki
 * Duration
 * Manga: Chapter #678-Chapter #690
 * Outcome: Black Zetsu uses itself and Madara as a medium to revive Kaguya. Obito is killed by Kaguya. Black Zetsu and Kaguya are sealed in a new moon. Team 7 and the Tailed Beasts returns to Earth. Allied Shinobi Forces Victory.

The Infinite Tsukuyomi is cast upon the world. Sasuke shields himself, Naruto, Kakashi, and Sakura. All others except for the reanimated Hokage are trapped in a dream and wrapped into the God: Nativity of a World of Trees, their chakra acting as fuel for their own confinement. The four emerge from Sasuke's protection, the last resistance against Madara. Before they can have their final battle, Black Zetsu, once more in control of Obito's body, transfers to Madara and takes control of him instead, converting him to Kaguya Ōtsutsuki. Kaguya transports them all to another dimension filled with lava, wishing to eliminate the only remaining obstacles. Together, Naruto and Sasuke proved difficult so she decides to separate the duo by sending Sasuke away. Obito has been recovered and helps Naruto's clone and Sakura to get Sasuke out of the deserted dimension. Elsewhere in a real world where the four reincarnated Hokage found Madara's lower half body and trying to find a way to stop Infinite Tsukuyomi, Hagoromo's spirit manifested from the lower half. With Naruto able to distract Kaguya and Black Zetsu into attacking him and his clone army, Obito and Sakura is able to get Sasuke out of the deserted dimension. With Naruto and Sasuke reunited, Kaguya sends everyone to a desert dimension where the heavy gravity could pin even herself down. Using this to her advantage, she attempts to kill both of them with her All-Killing Ash Bones, but Sasuke and Naruto are protected by Kakashi and Obito respectively. Obito used his Kamui to warp away the bone before it killed Kakashi, allowing himself to be slain. Using his sacrifice to his advantage, Sasuke initiated an attack, leading Kaguya to warp everyone to her main dimension. Saddened by Obito's sacrifice and enraged at Black Zetsu's mockery, Naruto joined Sasuke in the assault, severing Kaguya's left arm and with it Black Zetsu. Pinning Black Zetsu to the ground, Naruto and Sasuke continued their assault until Naruto threw multiple tailed beast Rasenshuriken at Kaguya. Taking the hit, the tailed beasts' chakra began reacting violently, before expelling out of her body in a giant mass of chakra, with the faces of all the tailed beasts. The unstable entity attacked Team Kakashi with chakra arms, with Kakashi saving Sakura from one arm using his new Susanoo, thanks to Obito's spirit for giving him his two Sharingan to battle Kaguya and leave the dōjutsu to Kakashi. With Kaguya is resealed again, along with Black Zetsu, Hagoromo summons the spirits of the other Kages to help other four reanimated Hokages get the jinchuriki and Team 7 out of Kaguya's dimension, with Madara also revert into normal states, and thus, the world is saved, thanks to Team 7's efforts.

Trivia

 * Itachi Uchiha was noted to have prevented an earlier potential outbreak of the Fourth Shinobi World War by carrying out the Uchiha clan massacre.
 * A Fourth Ninja War was also declared by Hiruko in the third Naruto: Shippūden movie, and would have pushed through if not for the efforts of the Konoha 11.
 * In the ending of Naruto Shippūden: Ultimate Ninja Storm 3, the Allied Shinobi Forces prevailed over Akatsuki. Tobi (with his identity still in secret), Madara and Kabuto retreated which in turn prevented the revival of the Ten-Tails, thus making the game's story ending non-canon to the anime and manga. This was due to the war still on-going in canon storyline.
 * So far, the Fourth Shinobi World War has stretched across three story arcs: Shinobi World War Arc, Ten-Tails Revival Arc, and Infinite Tsukuyomi Arc.