The plot of the film connects with it's prequels. For more information on the prequels' plot, see Krrish and Koi... Mil Gaya.

Krrish 3 sees Hrithik Roshan take on evil mutants and save the world from destruction in his superhero avatar.

In the first half, Vivek has his own look and his own den, a very modern facility which is visible in the trailer. He then changes himself in the second half. Here, he has extraordinary powers and he doesn’t know why he has them. He is handicapped and is able to cure himself. He is pitted against this world, against human beings and there is reason for this. The mutants are called maanvar — a combination of maanas and jaanwar — and have been created by Kaal through an experiment. Being a superhero, Krrish has to fight these beings with unknown powers.