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A van carrying undocumented immigrants across the border is stopped by INS agents when strange men wearing black suits arrive. The strange men, Kay and Dee, take one of the immigrants into the desert and order the others to continue to the United States. Finding nothing suspicious about that, the INS agents go home, and the movie ends with them enjoying an iced grande caramel macchiato while catching up on Better Call Saul.
Or that's what should have happened.
Instead, INS Agent Janus follows the two strange men into the dark desert to discover something otherworldly. The "illegal alien" is in fact an "illegal alien" of the outer space variety. The alien attacks, and when Dee's unable to stop it, Kay shoots it in an explosion of extraterrestrial entrails. Using a device called a neuralyzer, Kay wipes the memories of all the INS agents, and when Dee decides it is time to retire, Kay erases his memory, too.
Cut to New York City, where Detective James Edwards chases a perp with supernatural athletic abilities. Edwards corners him on top of the Guggenheim Museum. The criminal warns him the world is going to end and then jumps to his death without providing any of the necessary details like when or how or why.
Meanwhile, in upstate New York, a truck is struck by a crashing UFO. The truck's owner, a farmer named Edgar, investigates and a creature attacks him. The alien skins him alive to craft a human disguise, like something from the Buffalo Bill Etsy store.
Kay interviews Edwards about his experiences and takes him to Jake Jeebs' pawn shop. There, he outs Jeebs as an extraterrestrial by shooting off his head (it grows back) and forcing him to show his cache of imported and highly illegal alien weaponry. Edwards identifies the gun the perp had. Outside, Edwards tries to figure what's just happened. Kay erases his memory but invites him to a meeting.
The next morning, Edwards undergoes a series of tests. He passes, likely due to them grading on a creativity curve, and is offered a spot on the Men in Black. After spending the night weighing his options, Edwards agrees to the offer. His identity is expunged and he's given the codename Agent J.
They must've thought about that one for a while.
Meanwhile, the Edgar Bug (remember him, from upstate NY?) kills an exterminator (get the irony?) and steals his truck to drive into Manhattan Island. There he kills an Arquillian prince disguised as a human jeweler and steals what he believes is something called "the Galaxy."
After helping a squid alien give birth (just part of the job, folks) and interviewing Edgar's widow, Jay and Kay learn that a Bug has infiltrated the planet. (Kay hates bugs—they're the worst type of aliens.) They visit the morgue and discover Rosenberg's body. Rosenberg, more specifically the tiny alien living inside his head, warns Jay that he must find the Galaxy on Orion's belt to prevent war.
Puzzled, Kay and Jay visit Frank, an alien disguised as a pug. Frank tells them the Galaxy is the best source for subatomic energy and if the bugs get hold of it that'll be the end of the Arquillians. He also informs them that they're looking for something tiny, like a jewel.
Jay figures out that Orion is the name of Rosenberg's cat. They head back to the morgue to retrieve it, but the Edgar Bug was one step ahead. He steals the Galaxy and takes the deputy medical examiner, Dr. Laurel Weaver, as a hostage.
Back at MiB headquarters, the Arquillians send a warning that if the Galaxy is not handed over to them in one standard galactic week (a.k.a. one hour) they'll destroy the Earth. Jay figures out that the bug plans to escape from Earth on the UFOs disguised as observation towers at Flushing Gardens.
Laurel manages to free herself just as Edgar Bug climbs into a UFO. The ship takes off, but Kay and Jay arrive just in time to shoot it down. Crawling out of his crashed ship, the Bug takes off his Edgar suit and attacks them. Kay orders Jay to keep the bug on Earth and then trash-talks his way into the insect's stomach. Lucky for him, the Bug's mom never taught him how to chew his food.
Jay tries to overpower the bug but the alien's too much for him. He tries stomping on cockroaches just to taunt the bug and hopefully distract him from digesting Kay. It works. Just as it's about to kill Jay, Kay shoots his way out of its stomach, having retrieved both the Galaxy and his gun. Laurel finishes off the bug's upper half with Jay's weapon.
Back at MiB headquarters, Kay admits he hasn't been training Jay as a partner but as his replacement. Jay neuralyzes his mentor and reunites him with his wife, claiming he's been in a coma for 35-years. Jay becomes a top agent for the Men in Black, and Laurel joins as his partner, Agent L.
As the two drive off into the sunset, it's revealed that our universe inhabits a glass ball very much like the Galaxy, and a giant alien uses it to play marbles with it. Yep, that's how it ends.
Warning: Existential crisis imminent for anyone who ruminates for too long on this one.