Men in Black (MIB) Agent H (Chris Hemsworth) and London branch director High T (Liam Neeson) arrive at the Eiffel Tower to take out an alien invasion from the creatures calling themselves The Hive. If unleashed, they can wipe out everything in their path. After neutralizing and shooing away a couple, H and T fight their way into a passage in the tower that leads to The Hive’s base of entry. The agents arms themselves as the doors open, and the creatures emerge from the other side.
In a flashback to 20 years earlier in Brooklyn, New York City, little Molly Wright (Mandeiya Flory) watches as two MIB agents talk to her parents outside as they are looking for a creature known as a Tarantian. Unbeknownst to them, the creature is in Molly’s room, but she sees it as adorable and harmless. The agents neutralize Molly’s parents, but this moment changes her life.
As an adult, Molly (now played by Tessa Thompson) has been going through different agencies trying to uncover the secret organization that she has been obsessed with finding since that fateful night, all while working a dead end desk job. She catches a reading of an anomaly on her computer, and she follows the reading to a street in New York where a hidden entry is uncovered when pigeons fly through but disappear. Molly enters and watches MIB agents at the scene of an alien sighting. She finds a black suit and tries to sneak into the MIB headquarters, but she is scanned and identified as an unknown intruder. Molly is then met by Agent O (Emma Thompson) when the other agents take her in and attempt to neutralize her. She saves herself by revealing that she knows all about them after what she saw, and she must have some qualifications to join since SHE found THEM. O is unconvinced until Molly says that she has no life and nothing to live for, and uncovering the truth might give her a purpose. O decides to allow her in as a probationary agent and gives her all that she needs to now become Agent M.
In London, H is attempting to catch a known alien gangster during a card game, but he is outed as an MIB agent, and things get out of control as a venomous three-headed worm is set loose upon the place. The other aliens are killed, and both H and the head gangster are bitten, with the gangster’s assistant holding the antidote. H convinces her he will give her anything for the cure…so they sleep together.
Meanwhile, two alien creatures from the race known as Dyads (Laurent and Larry Bourgeois) arrive on Earth and steal a man’s identity after killing him. They encounter small aliens of the Pawn race and order that their queen be sacrificed. The queen’s protector, Pawny (Kumail Nanjiani), attempts to defy the Dyads, until they make their seriousness known.
M is sent to London via MIB’s special subway. There, she meets High T and learns of MIB’s monitoring alien activity from areas far outside the U.S., and they have been made aware of the Dyads’ arrival on Earth, and as they are from a planet close to The Hive, the agents fear they may strike again. M soon sees H as he enters a meeting where T tells the agents that a member of the Jababian royal family, Vungus (Kayvan Novak), wants the agents to show him a good time. H is assigned to be Vungus’s chaperon, and M manages to get herself in as his partner to join him on the case.
M and H go to a nightclub to meet Vungus. H attempts to hook M up with Vungus, but she refuses. The Dyads show up there and infect Vungus with some kind of poison. As his guards bring him out with the agents following, Vungus’s car gets blown up in the street. The Dyads emerge and attack, so M and H break out the big guns to fight back. However, the aliens prove to be almost un-killable, as the just absorb whatever energy the MIB hit them with. M goes to Vungus, who gives her a small crystal to keep in her protection. He doesn’t trust H and thinks there’s a threat within the MIB, and he dies soon after. The Dyads disappear, and the agents are met by Agent C (Rafe Spall), who chews them out for the disastrous outcome.
M and H meet with C and T in the aftermath. C suggests they fire and neutralize M, but H defends her. She brings her suggestion to T that someone in MIB could be a mole. T has more doubts in H’s capabilities, as everyone thinks he isn’t the same agent he once was. M and H then investigate the poison that Vungus was injected with, as H knows where it can be found. Meanwhile, C is shown surveillance footage of M in possession of the crystal.
The agents travel to Marrakech where they find Nasr (also Kayvan Novak), a known dealer who has a living alien beard named Bassam (ALSO Kayvan Novak). They bring up H’s relationship with a notorious alien arms dealer named Riza (Rebecca Ferguson). After the agents leave them, Nasr and Bassam spot the Dyads walking by. Nasr then orders Bassam to call Riza.
M and H come across a shop where they find a dead body and a secret entrance where they find the dead Pawns, save for Pawny. After the queen dies, he over-dramatically tries to kill himself, but M convinces him to help them since he is a witness, and Pawny pledges allegiance to M. They leave, and H shows M that he took the crystal from her, and he’s disappointed that she didn’t trust him enough to let him know. They then spot MIB agents approaching them as they were sent by C. They run back to Nasr and are given a hover bike to get them through the crowd. They escape the town but crash into the desert. T finds C’s tactics unethical and makes him consider that he is the mole. C thinks it’s H who can’t be trusted, but T still has faith in him.
The three discover that the crystal is a super-compressed star that has been designed to be a powerful weapon of mass destruction, which could prove deadly in the hands (or tentacles) of The Hive. They witness its power at the lowest setting when M accidentally activates it and makes a canyon in the sand. They set up camp for the night and bond for a bit until they find that Bassam stowed away in their canteen, and he steals the crystal to take to Riza. The agents and Pawny fix the hover bike and fly to Riza’s fortress.
Upon arriving, H uses Pawny as a peace offering and trade for the crystal to Riza. She is still hung up on their break-up, and so she double-crosses H and tries to have him sent off the island by her henchmen. However, H fights them off and runs back. M makes her way into the fortress and fights Riza while H fights her Tarantian bodyguard Luca (Spencer Wilding). Riza orders him to kill them until M learns he is Tarantian, and she repeats a phrase that the little Tarantian taught her as a child. Luca realizes who M is, and he turns on Riza, but the agents let her off once she gives them back the crystal.
As the agents prepare to leave, H tells M that his real name is Henry. Soon, they are cornered by the Dyads. H vows to protect the planet from The Hive, to which the Dyads reply that they are as well. MIB agents then show up and vaporize the Dyads with high voltage weapons. T comes out and congratulates the agents on their success.
The other agents celebrate the victory, but M and H feel that something is suspicious after the Dyads indicated they were never working with The Hive. After their case file is found to be deleted, M, H, and C all begin to realize that T might be the actual mole in the organization, but they need to keep it on the low and stop whatever he has planned. M, H, and Pawny take a car-ship-vehicle out and head to find him.
C guides the agents to a portal from The Hive has been opened in a nearby sector, in the Eiffel Tower. As they head to the site, M asks H how he and T first beat The Hive, but he only repeats the same exact phrase that has ever been used in describing the event (“with nothing but our wits and Series 7 de-atomizers”), leading them to realize that H was neutralized and that The Hive infected T before going into hiding and waiting for the right moment to strike back. They find T, who morphs into the Hive alien and attacks the agents. He takes the crystal and attempts to activate the weapon to destroy the planet. H attempts to reach into T’s true human side, just as M gets knocked into the portal. Pawny jumps in and rescues him by pulling her back and flying with his jet pack. T appears to break through briefly, just moments before M gets her hands on the super weapon and sets it to the highest power, blasting the creature into goo and destroying The Hive’s whole base.
M and H are met by O, and they all mourn the loss of T. She them promotes M to a full time agent, and makes H the probationary director of the London branch.
The two agents return home, and, now joined by Pawny, they head out in their car for another mission.