Agents J (Will Smith) and K (Tommy Lee Jones) are back…in time. J has seen some inexplicable things in his 15 years with the Men in Black, but nothing, not even aliens, perplexes him as much as his wry, reticent partner. But when K’s life and the fate of the planet are put at stake, Agent J will have to travel back in time to put things right. J discovers that there are secrets to the universe that K never told him – secrets that will reveal themselves as he teams up with the young Agent K (Josh Brolin) to save his partner, the agency, and the future of humankind.
On July 16, 1969, Agent K (Tommy Lee Jones) apprehended the intergalactic criminal Boris the Animal (Jemaine Clement) at Cape Canaveral in Florida before setting up the ArcNet shield, which protected Earth from an invasion by Boris’ species and rendered them extinct. Over 40 years later, Boris escapes from the LunarMax Prison facility on the Moon and arrives on Earth, intent on taking revenge on K – who took away his left arm during his arrest. After investigating a spaceship crash in New York City, K and Agent J (Will Smith) attend to the MIB Headquarters so K can give a speech about Zed after his death.
K and J go to a restaurant in New York City and discover that most of the customers there are aliens. This results in a fight between the Agents and the Aliens. In the kitchen, K finds Mr. Wu dead by getting shot by Boris. Meanwhile, J attempts to fight an alien fish. After killing him, he meets up with K in the roof and fight Boris with K. After failing to kill K and J, Boris tells K that he is already dead. K refuses to tell J about the incident at Cape Canaveral. That night, K talks with J on the phone and after J hangs up, K gets a weapon to protect himself from Boris. However, K suddenly disappears from his apartment.
The next day, J notices that K is no longer in his apartment. He finds out that a woman and a child live there now He arrives at MIB headquarters to discover that nobody knows K except for O. She tells him that K has been dead for over 40 years Agent O (Emma Thompson) , the new Chief after Zed’s death, deduces that there has been a fracture in the space-time continuum based on J’s insatiable craving for chocolate milk to ameliorate his headaches. J comes to the conclusion that Boris acquired a time-jump device and traveled back to 1969 to kill K, resulting in an inevitable invasion of Earth due to the absence of the Arc Net. J goes to Jeffrey Price (Michael Chernus), a black market dealer who sold Boris the time-jump device, and acquires one of his own with the goal to find the younger Boris and end his life in the hopes of saving K and the Earth. As the time-jump device needs a certain amount of velocity to activate, J must jump off the Chrysler Building to make the time-travel. He travels to July 15, 1969 – one day before the incident involving Boris and Agent K.