The noise the neuralyzer makes when it flashes is the sound of a strobe flash reloading. Sound editor Skip Lievsay filtered/modified the sound through a Synclavier synthesizer to make it more high-tech.
J's line on the "driver airbag" ("Actually it came with a black dude, but he kept getting pulled over.") was improvised by Will Smith. The producers liked it so much it even made the theatrical trailer. Barry Sonnenfeld however was not happy, it was played over and over in the month of June prior to the film's release, making the joke old and tired by the time people saw it in the movie.
Barry Sonnenfeld took issue with the producers wanting to focus on the love story between Agent J and Laura: "I learned on Wild Wild West (1999) that audiences didn't want to see Will Smith as the straight man. And until Tommy Lee Jones comes back into the movie, by definition, Will's the straight man."
When J and K are watching the Light of Zartha video in Newton's room, J comments on the corny video, saying "Looks like Spielberg's work". It's a light-hearted jab at Executive Producer Steven Spielberg.
The extra head attached to Scrad is called a 'symbiote,' and was first developed in Men in Black: The Series (1997). It is the most obvious development of the animated series to be carried over into the movies.
In an interview with Will Smith and Tommy Lee Jones, Smith said: "It was great working with Frank the Pug in the first film, but since we came back he's been acting like an a-hole." Jones then said, "Yeah, Frank's had a bit of an identity crisis since the neutering."
Famke Janssen was originally cast as Serleena, and even completed some of the filming, but was forced to drop out of the project due to a death in her family. Lara Flynn Boyle was then cast in her place.
The children of the cast/crew make an appearance in the film: - the little girl at the post office who wants to buy Rugrats (1990) stamps is Barry Sonnenfeld's daughter Chloe Sonnenfeld. - Tommy Lee Jones's daughter appears in the film as the little girl in the apartment where J, K, and the worms acquire weaponry. and the two children who look up as the MiB car flies overhead are Will Smith's kids.
In the Hungarian-dubbed version Elizabeth (the Young Girl at the Post Office) lines were redubbed from "Twenty Rugrats stamps please" to "South Park stamps please" because South Park (1997) was better known than Rugrats (1990) in Hungary that time. In the German-dubbed version her lines were re-dubbed to "Pokémon stamps please" because Pokémon (1997) was better known at that time.
The locker that holds the tiny aliens who worship K is numbered C18, the same number of the locker used in the film Get Shorty (1995) that contains the "dirty" money. Both films were directed by Barry Sonnenfeld.
The train locker is a tribute to the gangster mystery Once Upon a Time in America (1984), where a main character (Agent K, Noodles) returns after a long time, and tries to solve a long-ago mystery; notably, the train locker contains a vital clue to solving the mystery.
The steering mechanism in the car when flying near the ending scene is a silver-colored DualShock, the controller used for Sony's Playstation and PS2 consoles. This leads to J's joke about a "Gameboy".
The stickers on Scrad's/Charlie's fridge door: "LOSER" "MY OTHER CAR - IS A SKATEBOARD - ALTERNATIVE PRESS" "HARASSING ME ABOUT MY SMOKING MAY BE HAZARDOUS TO YOUR HEALTH" "Your Kid's An Honor Student - But You're A Moron" "The Truth is NOT out There!" "BARTHAT - *SUCKS* - TIGERMASK - ..." "NEW YORK - MAFIA" "Greetings from New York City" (on postcard showing a heist)
During the scene in Jeebs' (Tony Shalhoub's) store, among the many UFO genre items is featured a set of circa 1950s "Saucer" Ceiling Lamps, made by the Eames Company from their Atomic Collection. This is an apparent upgrade from the first film, which featured a vintage Atomic table lamp instead.
When K first meets Laura at the pizza shop, he remarks on a picture of Ben and says "That is a hell of a fish!" Tommy Lee Jones made almost the same remark of a picture with the main antagonist in the film The Fugitive (1993).
Osseus Labyrint: In one scene in MiB headquarters, two aliens in black bodysuits can be seen walking around on all fours with their limbs straight, bobbing their heads up and down. The two aliens are played by an interpretive dance duo, who toured with the band Tool, and appeared in the band's video for "Schism" performing the same move.
The trivia items below may give away important plot points.
The original ending of the film included a scene in which the World Trade Center towers opened up, releasing a swarm of UFOs into the air. Following the 9/11 terrorist attacks, the film's ending was changed. Unfortunately, this meant the film had a shorter running time, so when it was shown in theaters it was packed with trailers and the short film The Chubbchubbs! (2002) to fill the gap.
According to K, it rains when Zarthans cry. Three scenes are shown where it rains: when Laura cries; in K's memories where he is seen with Princess Laurana; and at the end when it rains inside Laura's spaceship.
The end shot seemingly implies that the audience have actually only seen a tiny part of the MiB operations complex in the first two films, and that the secret operation is on a previously unknown gigantic secret scale.