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The Men in Black are recurring characters in Code Lyoko. They are government agents who kidnapped Aelita's mother and continue to haunt Aelita's nightmares.
In the Show
Throughout season two the same three Men in Black are constantly shown in Aelita's nightmares and flashbacks. Their origins were explained more in the episode "The Key". Franz Hopper (Aelita's father) created Lyoko to counter project Carthage which was a military program used to block enemy communications. The Men in Black later arrive at their house to arrest them however Aelita and Franz Hopper escape to Lyoko.
In the episode "False Lead" XANA uses Jeremy's computer to hack a military weapons manufacturer. This leads two agents to show up to look for them. They arrive at the factory to arrest Jeremy however X.A.N.A. posses them to kill Jeremy and Ulrich. However his plan is foiled by Aelita deactivating the tower on Lyoko. The agents memory of the attack were erased by the return to the past option.
In the episode "Crash Course" X.A.N.A. creates a polymorphic clone of a Men in Black agent to attack the Lyoko warriors however he disappears after the tower is deactivated.
In the episode "Distant Memory" Aelita has a flashback to the day where they took her mother. While Aelita was playing in the show she got lost. When she found her way back home she witnessed over a dozen Men in Black (most of their bodies were silhouetted so only part of their faces and sunglasses were visible) kidnap her mother and drive away with her in a SUV.