Plot
In 1996 Brooklyn, Molly Wright witnesses her parents being neuralysed by agents of Men in Black while she helps an alien escape, avoiding neuralysation herself. Twenty-three years later, rejected from government agencies due to her "delusions" regarding alien life, Molly tracks down an alien landing and follows MiB agents to their headquarters in New York City. Caught entering the agency, Molly makes an impression on Agent O, arguing that she has proven her skills and has no life outside her search for the agency. She is awarded probationary agent status as "Agent M" and assigned to the organisation's London branch.

There, M meets High T, head of the London branch, and Agent H. M learns that H and High T fought off an invasion of the Hive – a parasitic race who invade planets by merging with the DNA of the conquered species – at the Eiffel Tower in 2016, using a wormhole included in the original migration to Earth; H has since developed a God complex, unconcerned with his duties and only keeping his job due to High T covering for him. M arranges for herself to be assigned to assist H in his meeting with Vungus the Ugly, his close friend and alien royalty. During their night out with Vungus, they are accosted by mysterious alien twins able to manifest as pure energy. They fatally injure Vungus, who gives M a strange crystal before he dies, claiming that H has changed since they last met and cannot be trusted. M points out that few people knew Vungus' location, and he was likely betrayed by one of the agents present when High T assigned H to guard him. Nervous at the possibility of a traitor within MiB, High T assigns Agents C and M to conduct an investigation while H is demoted to desk duty, with evidence suggesting that the twins had DNA traces of the Hive.

H convinces M to join him in following a lead to Marrakesh, where they recover "Pawny", the last survivor of a small group of aliens attacked by the Twins. Pawny pledges loyalty to M, and they are trapped by MiB agents coordinated by C, who recovered video footage of Vungus passing the crystal to M and believes she is the traitor. With the aid of alien contacts Nasr and Bassam, H escapes with M and Pawny on a rocket-powered bike, and they learn that Vungus’ crystal is a weapon powered by a compressed blue giant. As they repair the damaged bike, Bassam steals the weapon and takes it to Riza Stavros, an alien arms dealer and H's ex-girlfriend. Travelling to Riza's island fortress, the trio attempts to infiltrate the base, but are caught by Riza and her bodyguard Luca Brasi. Luca, the alien M rescued as a child, returns the favour by allowing them to leave with the weapon while he keeps Riza contained. The three are cornered by the Twins, who are killed by High T and a group of agents.

Although the case appears concluded, H and M review the evidence and realise that the Twins' phrases suggest they required the weapon to use ‘‘against’’ the Hive, especially when the only evidence of Hive DNA was provided by High T. They discover High T has deleted the case file and not sent the weapon to evidence. C also realises High T's deception, and 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 the Hive’s defeat reveals he was neuralysed when the Hive converted High T into one of their own. The High T/Hive hybrid activates a wormhole to draw the Hive to Earth, but H draws 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.

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.