Board Thread:Theories and Speculation/@comment-34229190-20180105214007/@comment-34194151-20180105230749

The Genjutsu trapped the 3 pains, it is unclear if it trapped the Real Nagato. Nagato can control the Pains and percieve the world through them but I think at best you would have to trap all 6 pains and Nagato himself in order to completely take him out of the fight with genjutsu. If you genjutsu one pain he simply looks through the eyes of another Pain to see what is really going on. Visual Genjutsu also works against Pain, nothing to suggest that it wouldn't.