The Boglodite criminal Boris the Animal escapes from the LunarMax prison on Earth's moon, intent on going back in time and killing Agent K, who on July 16, 1969, had shot off one of his arms and captured him. After investigating a spaceship crash in New York City, and following a skirmish in a Chinese restaurant, K learns Boris has escaped. K regrets not having killed Boris in 1969, returns to his apartment, and then all traces of K disappear. Arriving at MIB headquarters, Agent J discovers that only he remembers K as being alive in the present day, while all other MIB personnel remember K as having been killed in action in the year 1969.
Agent O, the new Chief after Zed's passing, deduces from J's statements that a fracture has occurred in the space-time continuum. The two realize Boris must have time-jumped to 1969 and killed K, resulting in a now-imminent Boglodite invasion of Earth which is vulnerable due to the absence of the protective ArcNet which K had installed in 1969. Through electronics-shop owner Jeffrey Price, J acquires the same time-jump mechanism as Boris. After jumping off the Chrysler Building to reach time-travel velocity, J arrives in 1969 a day before Boris kills K.
J follows a clue to Coney Island, where 29-year-old Agent K arrests him. After fruitless questioning at MIB headquarters, K places J in a large machine. At the last second, J says he will tell the truth of his mission. As a team, they follow Boris' trail to a bowling alley and then to Andy Warhol's Factory, where they meet the prescient alien Griffin, who possesses the ArcNet. Griffin tells them the Boglodites destroyed his planet, and that he does not wish the Earth to suffer the same fate. Griffin warns the two agents of Boris' impending arrival and hurriedly leaves.
The Agents later locate Griffin at Shea Stadium, where he gives them the ArcNet and instructs them to place it onto the Apollo 11 lunar rocket launch occurring in less than six hours. Upon arriving at Cape Canaveral, the agents and Griffin are arrested by military police. A colonel, however, allows them to continue their mission after Griffin uses his precognitive power to show the colonel how important the agents are.
At the launch pad, J and K confront both the 1969 and 2012 incarnations of Boris. Modern-day Boris impales J with his spikes before they both fall off the pad; however, J uses the time-jump to travel back to the beginning of the fight and avoid the spikes before pushing the old Boris off the pad. Meanwhile, as K battles the younger Boris, he ruptures a hose, causing it to spray liquid hydrogen on Boris' left arm, freezing it before he shatters it. K then plants the ArcNet on the rocket and the protective shield deploys after leaving the Earth's atmosphere. In the process, present day Boris is incinerated by the flames from the rocket's boosters.
The Colonel congratulates K returning from the launch pad. As J watches from the distance, the younger Boris emerges and kills the Colonel. K shoots and kills the younger Boris instead of arresting him. A young boy named James exits a military vehicle looking for his father. He pulls out a pocket watch revealed earlier to have been passed down to Agent J by his father, making J realize that he is the Colonel's son. Unwilling to reveal his father's death, K neuralyzes young James, telling him his father was a hero.
J returns to the present day, where he meets his partner at a diner. There, he shows K his father's pocket watch and thanks him. The senior agent replies that "it's been a privilege". As they leave the diner, Griffin, a few seats away, tells the viewer all is well with the world, except for an imminent asteroid impact on Earth if this is the timeline where K forgot to leave a tip. But when K returns to leave his tip, the asteroid collides with an orbiting satellite instead of the Earth |