Sunita (Jiah Khan) is a medical student, working on a project about the human brain with her class. When she is denied access by her professor to the curious case of Sanjay Singhania (Aamir Khan), a man reported to have anterograde amnesia, because it is under criminal investigation, Sunita decides to investigate the matter herself.
It is revealed that Sanjay loses his memory every 15 minutes. He uses a system of photographs, notes, and tattoos to recover his memory after each cycle to remind himself of his mission: to avenge the death of his beloved Kalpana (Asin). He systematically kills the people who were tied to the murder. His main target is Ghajini (Pradeep Rawat), a notable social personality in the city, and the man directly responsible for Kalpana's death and Sanjay's condition.
Police inspector Arjun Yadav (Riyaz Khan) tracks Sanjay down and hits him unconscious. Yadav finds two diaries in which Sanjay has chronicled the events of 2005 and 2006.
The film flashes back to 2005 as Yadav reads the diary. Sanjay Singhania is the chairman of the Air Voice mobile telephone company. In the course of business, he sends his men to meet Kalpana, a struggling model of Mumbai, about putting up a billboard above her apartment. The owner of Kalpana's advertising firm misinterprets this as a romantic advance and, in view of a possible lucrative Air Voice ad campaign, encourages Kalpana to accept the overture.
Kalpana thinks of it as an innocent prank that may fetch her better modelling work and decides to charade as Sanjay's girlfriend. Sanjay goes to confront Kalpana about this but falls in love with her at first sight. He hides his identity and introduces himself as Sachin, and the two begin spending time together. The diary ends with Sanjay proposing to Kalpana and promising himself that he will reveal his actual identity if she accepts.
When Yadav is about to read the 2006 diary, Sanjay awakes and attacks him, tying him up. Ghajini realizes that someone is trying to kill him but cannot figure out who. Sunita visits Sanjay's flat and discovers Sanjay's plan to kill Ghajini. She takes both his diaries before finding Yadav, beaten and bound, and freeing him.
Just then, Sanjay arrives, but he remembers neither of them and chases them out. Yadav is hit by a bus as he flees in terror, and Sunita, believing Ghajini is the good guy in danger, informs him about Sanjay. Ghajini arrives at Sanjay's flat and destroys all of Sanjay's photographs and notes, as well as the tattoos on Sanjay's body, so that Sanjay is left with nothing to help him recover his memory.
As Sunita reads the diaries, the film flashes back to 2006, where it is revealed that Kalpana had accepted Sanjay's proposal. When this diary ends abruptly, Sunita digs further and discovers that Kalpana was travelling to Goa for a modelling assignment when she came upon 25 innocent young girls being trafficked. She had saved the girls, who named Ghajini as the ringleader of the racket. Outraged, Ghajini broke into Kalpana's apartment with his goons to kill her. When Sanjay arrived, he found Kalpana stabbed. Ghajini then hit Sanjay over the head with an iron rod.
Sanjay's last sight was Ghajini brutally murdering Kalpana with the iron rod. Kalpana's last word to Sanjay was "Ghajini."
Sunita, now aware of the shocking truth, finds Sanjay in the hospital and tells him the truth. He flies into a heartbroken rage and tracks down Ghajini with Sunita's help. He fights off all of Ghajini's henchmen with a superior and anger-fueled strength.
Ghajini, realizing Sanjay is too strong for him, flees. Sanjay's memory loss strikes again, and he forgets who Ghajini is. Ghajini takes this opportunity to stab Sanjay and taunt him with the grisly tale of how he murdered Kalpana. As he is about to make Sanjay relive the experience by killing Sunita the same exact way, Sanjay recovers the memory of Kalpana's death, and overpowers Ghajini in a flash of strength. He finally kills Ghajini, in the same way Ghajini had killed Kalpana.
The film ends with a still-amnesiac Sanjay volunteering at an orphanage. Sunita gives him a gift that reminds him of his bond with Kalpana, and Sanjay imagines Kalpana by his side, finally at peace with himself.
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