Plot

The MIB tackle a mole in their organization.

After an eye-opening encounter of the third kind, the secret MiB organisation's newest recruit, Agent M, finds herself under the wing of the heroic Agent H in cosmopolitan London, when a shape-shifting duo of intergalactic assassins executes an alien aristocrat. Now, with a devastating super-weapon of mass destruction hidden somewhere on Earth, the Men in Black will leave no stone unturned to retrieve it. However, heavy clouds of mistrust and a scent of betrayal envelop the once-incorruptible agency. Is there a well-placed mole in their midst?—Nick Riganas

All of the agents of a top secret government organization must be really cautious in everything that they do and say after they discover that there is a traitor among them. As they try to figure out who the traitor is, they must deal with their deadly missions as well.—RECB3

In Brooklyn in 1996, Molly Wright (Tessa Thompson) witnesses her parents being Neuralysed by agents of Men in Black while she helps an alien escape, avoiding Neuralysation herself as her parents assumed that she was asleep. Twenty-three years later, having been rejected in applications to government agencies on the grounds of her "delusions" regarding the evidence of alien life, she manages to track down an alien landing and track the MiB agents back to MiB headquarters in New York. Although she is caught upon entering the agency, Molly makes an impression on Agent O (Emma Thompson), arguing that she has proven her skills in finding out about the organization's existence and has no life outside of her search for the agency. Convinced, she is awarded probationary agent status as "Agent M" and assigned to the London branch of the organization.

Once in London, M meets High T (Liam Neeson), the head of the London branch, and manages to arrange for herself to be assigned to assist Henry / Agent H (Chris Hemsworth) in his meeting with Vungus the Ugly (Kayvan Novak), a member of an alien royal family who is a close friend of H. During their night out with Vungus, they are accosted by mysterious alien twins who can manifest as pure energy, who fatally injure Vungus. Vungus passes a strange crystal on to M before he dies, claiming that he cannot trust H with it as H has changed since they last met. Although Agent C (Rafe Spall) expresses disappointment for H's dealing with the situation, M points out that few people knew Vungus' location when he was attacked, which leads to the conclusion that Vungus' location was betrayed by one of the MiB agents present when High T assigned H to guard him. Nervous over the possibilities of a traitor in MiB itself, High T assigns C and M to conduct an investigation while H is demoted to desk duty, with the investigation suggesting that the twins had DNA traces of the Hive, a parasitic race who invade other planets by merging with the DNA of the conquered species. M learns that H and High T were responsible for fighting off a Hive invasion at the Eiffel Tower in 2016, using a wormhole included in the original migration to Earth, but since that time H has developed a God complex, demonstrating an uncaring attitude towards his duties and apparently only keeping his job due to High T covering for him due to the soft-spot they have for each other.

H convinces M to join him in following up a lead in Marrakesh, where they recover "Pawny" (Kumail Nanjiani), the last survivor of a small group of aliens who were attacked by the Twins. Pawny pledges new loyalty to M, but they are subsequently trapped by MiB agents coordinated by C, who has recovered video footage of Vungus passing the crystal on to M and believes that she is the traitor. With the aid of one of his alien contacts, H is able to acquire a rocket-powered bike and escape with M and Pawny, where they learn that the crystal Vungus gave M is actually a weapon powered by a compressed blue giant. As they repair the damaged bike, H's alien contact manages to steal the weapon and take it to Riza Stavros (Rebecca Ferguson), an alien arms dealer and H's ex-girlfriend.

Traveling to Riza's island fortress, the trio attempts to infiltrate the base and recover the weapon, but are caught by Riza and her bodyguard. However, the bodyguard turns out to be the alien that M rescued as a child and he returns the favor by allowing them to leave with the weapon while he keeps Riza contained. The three are cornered by the Twins once again, but the twins are killed by High T and a group of agents.

Although the case appears to be concluded, H and M review the evidence and realize that the Twins' phrases could suggest that they required the weapon to use against the Hive rather than to use it for the Hive, especially when the only evidence of Hive DNA was provided by High T. As Agent C concedes that the evidence favors the idea of High T's deception, he allows H and M to follow High T to the Eiffel Tower. As they travel to the wormhole, M's questioning of H's memory of his defeat of the Hive reveals that he was Neuralysed, which is confirmed when they confront High T. The Hive converted High T into one of them and Neuralysed H so that he could act as the 'hero' and conceal their true activities. The High T/Hive "hybrid" is able to activate a wormhole that will draw the Hive to Earth, but H is able to draw out High T's true personality long enough for M to use the weapon to destroy High T and the Hive infestation trying to reach Earth through the wormhole. With the truth of High T's conversion exposed, Agent O joins H and M in Paris, where she grants M full agent status and appoints H probationary head of MiB's London branch.