Scientist Rohit Mehra lives in Mumbai with his son, Krishna "Krrish" Mehra (both portrayed by Hrithik Roshan). Married to Priya (Priyanka Chopra), a dedicated journalist working for Aaj Tak, their family appears ordinary at first glance. Rohit is focused on a groundbreaking experiment at a government research institute aimed at reviving dead tissues using solar energy but continually struggles to perfect his work due to the intense sunlight challenges.
One day, while Krishna is juggling multiple day jobs—often losing them due to his superhero alter-ego, Krrish—he overhears a dire news report about a malfunctioning airplane with stuck tires, which poses a significant threat to the passengers aboard. Without hesitation, he transforms into Krrish and heroically intervenes, saving the aircraft from imminent disaster.
In a twist of fate, Rohit learns about a deadly virus wreaking havoc in Namibia, with no antidote in sight. Concerned, he reaches out to his colleague Dr. Varun Shetty (played by Arif Zakaria). However, their plans for a breakthrough are tragically disrupted when both Shetty and another scientist, Dr. Alok Sen (Asif Basra), are brutally murdered by Kaya (Kangna Ranaut), a shape-shifting mutant working for the villainous Kaal (Vivek Oberoi), who is a physically impaired genius with dangerous telekinetic abilities. Kaal's sinister experiments to cure his ailments involve creating "maanvars," hybrid creatures composed of human and animal DNA, marking a dire turn in their mission.
As the plot thickens, it’s revealed that Kaal has maliciously unleashed the virus in Africa to profit from the antidote he intends to sell. Amidst this chaos, Priya discovers she is pregnant, adding further urgency to their situation. Rohit finds that the virus inexplicably does not affect him, Krishna, or Priya. Ingeniously, he concocts an antidote using Krishna's blood and deploys it through strategically set explosions.
Kaal, seething with rage at this unforeseen paradigm shift, sends his mutants to hunt Rohit down. Krrish bravely saves his father, but tragedy strikes as Priya is injured and hospitalized. Krrish triumphs over the mutant Striker (Gowhar Khan), while Kaya—under Kaal's orders—kidnaps Priya and assumes her identity, misleading Krishna into believing they have lost the child.
Desperate for the truth, Rohit travels to Singapore to confront Dr. Siddhant Arya (Naseeruddin Shah) but is kidnapped instead. Meanwhile, Krishna uncovers Kaya's true form and furiously demands to see Kaal's laboratory. As Kaya begins to develop feelings for Krishna, she makes the decision to assist in rescuing Priya.
At Kaal's lab, shocking revelations unfold—Kaal is actually Rohit's son, born handicapped due to a horrific experiment conducted by Dr. Arya while Rohit was his captive. Initially abandoned, Kaal was adopted but has now turned to horrific methods to regain his abilities. Kaya, in an act of redemption, saves Priya, yet pays the ultimate price with her life at Kaal's hands.
In a turning point, Kaal eliminates Krrish but, motivated by the death of his son, Rohit re-attempts his failed experiment aiming to revive Krishna. Though this heroic act costs him his life, it successfully passes on his powers to Krishna, who must now confront Kaal. Facing threats against Mumbai’s safety, Krrish emerges more determined than ever and, after a series of intense confrontations, succeeds in defeating Kaal using his father's solar energy experiment.
The film concludes six months later, with Priya naming their newborn son Rohit, who astonishingly appears to inherit special abilities of his own.
