| Director | Rakesh Roshan |
|---|---|
| Budget | ₹100 crore |
| Box office | ₹393 crore |
Six years after getting rescued and returning to India with his son Krishna after eliminating Dr. Siddhant Arya, Dr. Rohit Mehra now lives with the former in Mumbai while the latter's mother, Sonia Mehra, has passed away in this time period. Krishna is married to Priya, who now works as a reporter for Aaj Tak after resigning from her previous job in Singapore, and Rohit works in a research institute. Krishna, while moonlighting as superhero Krrish, is regularly fired from various day jobs due to lack of attendance. Meanwhile, Rohit is researching a device that will bring dead tissues to life using solar energy (after realizing how Jadoo gave him powers derived from sunlight), but the experiment needs a filter that could pass only the amount of sunlight needed.
A deadly virus is spreading in Namibia whose antidote has not yet been discovered. Rohit's friend Dr. Varun Shetty and Dr. Alok Sen, a scientist who wants to reveal information about the virus, are murdered by Kaya, a shapeshifting female mutant. She is the secretary of Kaal, a handicapped evil geneticist with telekinetic powers. Kaal creates a team of human-animal hybrids called Maanvars (a portmanteau of two Hindi words, "Maanav" meaning human and "Jaanvar" meaning animal) with distinct physical powers to cure himself, but to no avail. The virus was spread by Kaal himself to incur huge profits by selling its antidote. On Krishna's birthday, Priya gives the good news of her pregnancy to Krishna and Rohit. Kaal sends his mutants to India to infect the population. Rohit discovers that the virus, now spreading through Mumbai, has no effect on Krishna, Priya, or himself. He decides to test it on Krishna. Rohit makes an antidote with Krishna's blood, which Krishna spreads over the whole city. Kaal sends his mutants to attack Rohit. Krrish saves Rohit, but Priya is injured. Carrying out Kaal's instructions, Kaya shapeshifts into Priya while Priya is kidnapped by Kaal. Posing as Priya, Kaya leads Krishna to believe that Priya miscarried in the attack. While discovering the truth behind the antidote, she starts loving Krishna one-sidedly and often feels guilty for cheating him.
Meanwhile, Kaal plans to have Priya have an early childbirth so that he could use the child's bone marrow to cure his disability. Kaya, disguised as Krishna, goes to Rohit's home lab, where Rohit reveals that he will travel to Singapore to meet Dr. Mathur, who used to work with Dr. Arya. Rohit hopes this meeting will help solve the mystery behind the virus. At the same time, Krishna walks to the lab to meet Rohit. Kaya, still disguised as Krishna, then transforms into Priya and lies to the real Krishna, saying Rohit is busy with his research work and shouldn't be disturbed. The next day, Rohit calls Krishna and tells him that he had sought every answer from Dr. Mathur. Krishna, unaware of all this, realizes that something is wrong and finds out that Priya has been kidnapped. He transforms into Krrish and confronts Kaya. Kaya finally agrees to help and leads him to Kaal’s secret lab, where Priya is rescued. It is revealed that Kaal is Rohit's biological son, created by an experiment conducted by Dr. Arya while Rohit was held hostage by him years earlier. He was born inheriting Rohit's powers but handicapped except for his face and index fingers. He gets adopted by a wealthy man whom he then kills.
Kaal uses Rohit's bone marrow to cure his disability. Kaya saves Priya but is murdered by Kaal for her disloyalty. Kaal also severely injures Krrish. Rohit reuses his failed dead tissues experiment to save Krishna. However, the beam of light created by the experiment needs a filter to take effect on Krishna. Rohit stands in front of it, allowing only a portion of it to make contact with Krishna. This resurrects Krishna, killing Rohit in the process. Kaal has returned to Mumbai to threaten its citizens should Priya not be found and taken to him. Priya voluntarily surrenders herself, but Krrish then arrives, and a fight between Krrish and Kaal ensues. With the two now capable of flight and super strength, Krrish and Kaal's fighting destroys many buildings across Mumbai, while Krrish is emotionally weakened due to the number of people dying around them. Finally, Krrish manages to kill Kaal using Rohit's solar experiment pen by focusing the unfiltered rays onto him. Six months later, in the aftermath, Krishna and Priya name their newborn son Rohit Mehra. The baby also seems to exhibit superpowers.