Years have passed since Krishna Mehra (Krrish) saved the city and won the heart of Priya. Now living a dual life in Mumbai, Krishna is no longer just a hero saving people from burning buildings; he has become a symbol of hope for the entire nation. He balances his job at a research institute with his secret identity, often aided by his father, the genius scientist Rohit Mehra.

In a dark, high-tech laboratory hidden in the mountains, Kaal, a evil genius suffering from a debilitating physical condition, plots world domination. Kaal possesses immense mental powers—telekinesis—but his body is withered. He believes that the key to his cure, and ultimate power, lies in the DNA of Rohit and Krishna. Kaal creates an army of "Maanvars"—beings that are a genetic hybrid of humans and animals. They are strong, fast, and blindly loyal.

Hrithik Roshan returns as both the shy genius Rohit and his heroic son Krrish, now facing his most formidable enemy yet: Kaal, a sinister megalomaniac played with chilling intensity by Vivek Oberoi. Kaal creates an army of genetically mutated human-animal hybrids, unleashing chaos across the city.

To feed his insatiable greed and desire for global dominance, Kaal unleashes a deadly, artificially engineered biological virus across international borders, targeting densely populated urban areas.