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.