In 2016, Agents H and T are sent to stop an invasion of the Roy, a parasitic race that entered the Eiffel Tower in Paris via a wormhole.
23 years ago, Molly Wright, living in Brooklyn, sees her family being neuralized by Agents and escapes her own neuralization by kidnapping an alien.
Twenty-three years later, Molly attempts to join the FBI and CIA as an undercover agent, but is viewed as strange because of her stories about alien life. Luckily, he finds a trail to find the Alien Secret Agency (MIB) and attracts Agent O's attention. When Agent O sees that Molly has proven her skills and dedication to the Agency, he grants her "Agent M" status and assigns her to the London branch.
When he arrives in London, he meets Agent M, Agent H and Agent T. Agent H is an arrogant and responsibility-avoidant agent, but he is protected by Agent T.
One day, Agent H and Agent M are assigned to protect the alien Vungus, Agent H's friend and royalty. However, mysterious twin aliens kill Vungus and give Agent M a crystal.
Agent M learns that the crystal is a superweapon and convinces Agent H to find it. Along the way, they escape a group of aliens and suspect Agent T of protecting Agent H.
Eventually, having found the superweapon, Agent M and Agent H rescue it from alien arms dealer Riza Stavros. However, Riza makes plans to put the gun at Roy's disposal.
Agent M and Agent H work together to stop Riza and eventually defeat her and Roy. Agent T is revealed to be Roy's agent and is killed by Agent M.
For his bravery, Agent M is accepted as a full agent by Agent O, and Agent H is appointed temporary manager of the London branch.