A sequel to 'Koi Mil Gaya', Krrish is the story of Krishna, son of Rohit (Koi Mil Gaya) who stays with his grandmother (Rekha) in Manali. Rekha protects Krishna from the outside world as she does not want the world to know about Krrish's supernatural powers, which he has bestowed from his father. Priyanka comes to Manali on an adventure journey and meets Krishna. Both fall in love. Priyanka goes back to Singapore and Krishna follows her to Singapore to meet her mother and get her back to Manali.

Naseeruddin Shah, a scientist, is also in Singapore and is in the process of re-building a super computer which was built by Rohit. Krishna also learns that his father is also alive and is kept captive with Naseeruddin Shah. How Krishna stops Naseeruddin Shah and rescues his father forms the climax of the story.