Sage Mode

Sage Mode is the result of using natural energy along with a ninja's normal chakra in perfect balance to drastically empower their abilities.

Usage
A prerequisite to being able to use senjutsu is that the user must have a large reservoir of chakra themselves in order to manipulate the natural energy.

Advantages
There are numerous advantages while using toad Sage Mode. These include:
 * The user's physical strength, speed, stamina, reflexes, and durability dramatically increase.
 * The user's ninjutsu, genjutsu, and taijutsu become more powerful.
 * The user can harness the natural energy surrounding them, turning it into an extension of their body, which increases the reach of their attacks.
 * The user gains the ability to sense chakra around them.

Disadvantages
There are a few disadvantages while using toad Sage Mode. These include:
 * If the user draws in too much natural energy in the attempt to initiate Sage Mode, they run the risk of transforming into a toad, then into stone. If the transformation is completed, it cannot be reversed.
 * In order to gather enough natural energy to initiate the transformation into Sage Mode, the user must remain perfectly still. Because of that, the user can be an easy target for an opponent.
 * Because the user needs to move during combat, the senjutsu chakra cannot be replenished, which means the user can't stay within this state for extended periods of time.
 * The second and third weaknesses mentioned above can be bypassed through the Sage Art: Amphibian Technique, where one Sage gathers chakra for another or as in Naruto's case, shadow clones can be used for the same purpose.
 * After Sage Mode has ended, the user appears to experience exhaustion.

Imperfect Toad Sage Mode
Jiraiya was not able to properly balance his own chakra with natural energy, resulting in him using an imperfect form of Sage Mode. As a result of the imbalance (and the imperfect nature of his transformation), Jiraiya took a number of toad-like traits when using Sage Mode. His appearance was altered: his nose grows bigger and gains warts, he gains excess hair (his goatee), and toad-like eyes. Further transformational attributes includes him taking on a toad-like stature and the lines on his face become much thicker, taking over each side of his face. Because of these traits, Jiraiya didn't like to use Sage Mode as it "displeases the ladies". He also showed the ability to transform his limbs (e.g. his hands and feet) into those of frogs so as to aid in manoeuvrability.

In order to get around the danger of remaining stationary during a battle to re-enter Sage Mode, Jiraiya would summon Shima and Fukasaku by drawing a blood contract on his face. The Two Great Sage Toads would fuse to Jiraiya's shoulders with the Sage Art: Amphibian Technique, gathering natural energy from their stationary positions on Jiraiya's shoulders for him to use.

Perfect Toad Sage Mode
Unlike Jiraiya, Naruto is able to perfectly balance the natural energy with his own chakra. This allows him to use the true Sage Mode, which retains all of his normal physical characteristics except for toad-like eyes: yellow irides, horizontal bar-like pupils, and reddish-orange pigmentation around the eyes; the mark of a true sage on each eye. A true sage would still suffer from the weaknesses of Sage Mode, requiring that they use Sage Art: Amphibian Technique in a battle situation. Because of the Nine-Tailed Demon Fox sealed within Naruto, however, Fukasaku was rejected whenever he tried to fuse with him.

As a workaround, Naruto has some of his shadow clones gather natural energy elsewhere while he fights. Once he has run out of his own senjutsu chakra, he has one of the clones disperse, giving him the clone's natural energy and allowing him to enter Sage Mode again. This method limits the maximum number of shadow clones that Naruto can create to five for as long as the clones are gathering natural energy, as anything more would interfere with their focus. To make sure he has enough shadow clones for use in battle, Naruto has only two shadow clones gather senjutsu chakra, allowing him to enter Sage Mode a total of three times. Naruto also stated that it is possible to lengthen the time he is in Sage Mode. He now can enter Sage Mode almost instantaneously.

During his meeting with Nagato, Naruto was stabbed in the gut with Nagato's chakra disruption blade. Nagato thought that he would be able to control Naruto with his own chakra, but Naruto revealed a fusion of his initial jinchūriki form and Sage Mode characteristics. The exact capabilities of this form are unknown, but it was strong enough to completely resist Nagato's control at a close proximity. The irides turn red and his pupil resembles that of both the fox's and his own when in Sage Mode, like a cross.

Advantages
There are numerous advantages granted while using snake Sage Mode. These include:
 * The user's perception abilities, reflexes and speed dramatically increase.
 * The user's ninjutsu becomes more powerful.
 * The user gains further access to snake anatomy, such as their brille, which can be used to lock out light as well as stop visual-based genjutsu from affecting them. They are also able to perform abilities that are characteristic of snakes, such as dislocating their jaw, although this is not exclusive to this mode.

Disadvantages
Like Toad Sage Mode, Snake Sage Mode has similar flaws in that moving too much would disable the user from drawing in natural energy and that remaining still to gather the needed energy leaves the user open to attack. However, for his Sage Mode, Kabuto assimilated the DNA of Jūgo to replicate his clan's ability to passively absorb natural energy, thus allowing him to continuously collect the energy even while moving.

Perfect Snake Sage Mode
While retaining most of his normal physical characteristics in Sage Mode, Kabuto Yakushi did display greater areas of darkened pigmentation of the markings around his eyes which tapered off rafter reaching his shoulder blades. More noticeably, he gained four horns growing out from the back of his head as well as darkened sclera.

Trivia

 * In the film Naruto 5: Blood Prison, the red coat Naruto wore during his return in the Invasion of Pain would appear when he enters Sage Mode. Like every other physical change with the form, it would disappear when he turned back to normal.