By 2002, Agent J (Will Smith) has become a top agent in the Men in Black force but has a reputation for neurolyzing partners who don’t measure up to his first partner, Agent K (Tommy Lee Jones). While investigating the murder of an alien named Ben (Jack Kehler) at his pizzeria, a waitress named Laura Vasquez (Rosario Dawson) tells him the murderers are Serlenna (Lara Flynn Boyle), a shapeshifting, plant-like Kylothian alien who has taken the form of a Victoria’s Secret model, and her two-headed servant Scrad and Charlie (Johnny Knoxville). They are searching for the Light of Zartha. Agent J is attracted to Laura and neglects to neuralize her memories.

No-one knows much about the Light of Zartha, except that it’s immensely powerful. Every time, his investigations seem to lead to J’s former partner K, who naturally remembers nothing. In Truro, Massachusetts, where K is now the postmaster, J convinces him to return by proving that all his employees are aliens. In New York City, Serlenna and Scrod/Charlie attack the MIB headquarters before J can reverse K’s neuralyzing, but alien pawnshop owner Jack Jeebs (Tony Shalhoub) has an illegal neuralyzer. K gets his memories back but remembers that he once neuralyzed himself to erase what he knew of the Light of Zartha, and still does not know anything about it. Still, he left himself some clues.

At the pizzeria, they find a locker key. J and K hide Laura with the worms while they go to Grand Central Station, where a society of tiny aliens in a locker worship K as their god. They have his watch and video-store membership card. At the store, they watch a movie about the Light of Zartha and K remembers that Zartha’s Queen Lauranna (Linda Kim) long ago entrusted MIB with guarding the Light from Serlennna, who killed Lauranna. K had neuralyzed himself because he was grief-stricken. He still can’t remember where he hid it or what it looks like. It must return to Zartha soon or Earth and Zartha will both be destroyed.

Laura has been taken from the worms’ apartment by Serlenna. J and K attack MIB HQ to free Laura and the other agents. Serlenna pursues them through New York in a spaceship but is eaten by a gigantic worm named Jeff who lives in the subway. Laura’s bracelet leads them to the roof of a skyscraper, where a ship is parked to transport the Light to Zartha. K reveals that Laura is the daughter of Lauranna (and of K) and she is the Light itself. K convinces her to go to Zartha and save both planets, Serlenna has taken the form of Jeff the giant worm and attacks the ship, but J and K shoot her down. To make New York forget this, K activates the giant neuralyzer in the Statue of Liberty’s torch. They discover that the human universe is really a tiny universe in a locker in an all-encompassing train station.

The film was directed, like the first one, by Barry Sonnenfeld. It was written by Robert Gordon and Barry Fanaro, based on the Marvel comic by Lowell Cunningham. Rip Torn died in 2019 and this was his last role in the series, though he had a cameo in Men in Black III because of special effects. The worms (voiced by Brad Abrell, Greg Ballora, Thom Fountain, and Carl J. Johnson) had a bigger role than in the first movie because they had been such a hit with the audience. Originally, the climax took place at the Twin Towers, but was re-filmed after the 9-11 attack. In fact, the towers were cut out entirely. The movie received mixed reviews, as sequels tend to do. It was nominated for a Visual Effects Society Award but lost to Lord of the Rings: The Two Towers. Lara Flynn Boyle got a Razzie.

The original Pug (voice of Tim Blarney) appeared in the sequel, but they dyed the gray fur around his muzzle to make him look younger. Famke Janssen was originally cast as Serlenna but dropped out because of a death in the family. Lara Flynn Boyle was hired because she was Jack Nicholson’s girlfriend and Sony wanted him in an Adam Sandler movie, Anger Management. Will Smith had bulked up for the film Ali (2001) and had trouble getting back into the Black Suit. J says to Serlenna, “I’m about to lay the smackdown on your candy ass,” quoting Dwayne “The Rock” Johnson. Michael Jackson had a cameo, playing Agent M. Rick Baker had a cameo, playing an agent at the Alien Registration Counter, in his trademark ponytail.