The intergalactic 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, and K regrets not having killed him. K returns to his apartment, where he and all traces of him disappear. Arriving at MIB headquarters, Agent J discovers that he alone remembers K as being alive in the present day, while all other MIB personnel remember K as having been killed in action in 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 an imminent invasion of Earth due to the absence of the protective ArcNet which K had installed in 1969. Through electronic-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 the 2012 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 largeNeuralyzer. At the last second, J says he will tell the truth of his mission. As a team, they follow 1969 Boris’ trail to a bowling alley and then to Andy Warhol’s Factory, where they meet the five-dimensional, prescient alien Griffin, who possesses the ArcNet. Being able to look into multiple probable futures, he warns the two agents of 1969 Boris’ impending arrival and hurriedly leaves.
The Agents 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 the agents to carry on their mission after Griffin uses his precognitive power to show him ‘how important they are’.