‘Bullet Raja’ is about a common man who transforms into a gangster revolts against the very system he once obediently followed by declaring war on the police, the government, and the industrialists.

Raja Mishra (Saif Ali Khan) gatecrashes into a marriage while trying to escape from a brawl. The bride's cousin, Rudra Tripathi (Jimmy Shergill), and Raja form a friendship upon Raja revealing that he is an uninvited guest. While in process of seducing the mujra dancer, Raja overhears a plot by Lallan Tiwari (Chunky Pandey) to execute everyone in the wedding upon instructions from a land lord wanting to use Rudra's uncle's land for poppy farming. Raja warns everyone about the impending attack and Raja and Rudra fight off the attacking Lallan Singh's gang. Rudra's uncle (Sharat Saxena) sees the potential in Raja and Rudra forming an alliance for offering protection to political personalities and offers them to join his gang. Not wanting to enter the world of politics, they refuse and Rudra's uncle advices them to take refuge from Lallan's gang in jail. In a later incident Rudra's uncle is killed by the poppy field owner with help of Lallan Singh.

They start working for Ram Babu Shukla (Raj Babbar), a politician, and in the process kill the poppy fields' owner, gain credibility and support in the political circles which brings them fortune and fame amongst youth. Their friendship and partnership is talk of the town making the otherwise preferred hitman Sumer Yadav rendering useless. While representing Ram Babu Shukla in an important meeting Raja and Rudra are insulted by Bajaj (Gulshan Grover). In order to teach him a lesson Raja and Rudra kidnap Bajaj while he is in process of pretend interviewing a girl named Mitali (Sonakshi Sinha) for the role of actress. They extort money from Bajaj and in process Raja started to develop feelings for Mitali. On advice of Shukla, Raja, Rudra and Mitali go to Mumbai until matters settle and avoid any attacked from Bajaj. Raja proposes to Mitali and Rudra approves of their relationship.

Raja takes his revenge by killing Bajaj which turns all political and business fraternity against him. They all want him dead in order to gain Bajaj's money which is needed to fund their election campaigns but is being held by Shirivastav. According to the plan, Arun will kill Raja, but then the mole will kill Arun to appease the youth that support Raja. Raja finds out about the plan and reveals it to Arun. Together, they kill the mole and fake Raja's death. In the end, it shows Raja leaving with Mitali for a new life.