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Men In Black
From Code Wiki
The Men In Black in Code Lyoko are mysterious agents who work as repressive operators against traitors in the Project Carthage. They were sent after Franz Hopper, who escaped to Lyoko with his daughter Aelita. In Distant Memory, it is revealed that the Men In Black kidnapped Aelita's mother (as many fans suspected), and Aelita is quite afraid of them for that very reason, often having nightmares starring a Man In Black or two.
In Season 3, it is learned they are from "a very secret section of the secret services" (according to them): even the president doesn't know they exist, and they themselves don't really know who commands them (that could mean they believe to be a governmental service but in fact serve private leaders). They obviously appear as a parody of conspiracy theories. To fit with all stereotypes, they always wear sunglasses, and are virtually beyond Jim's intelligence level.
After they kidnapped Aelita's mom, they pursued Franz and Aelita to the Hermitage, but when Franz felt them watching him, he took Aelita and went to Lyoko. It was then revealed to us that the reason they are after him, is that he was creating Xana and Lyoko to destroy Project Carthage because they were going to use it as a weapon to disrupt enemy communications.
In the credits of Season 2 and onward, we always see a file marked "Confidential" that has Franz's real name Waldo Scheaffer and contained pictures of him and his Project Carthage colleagues, then other pictures of him and Antea in the Mountain Cabin, and pictures of the Hermitage as well, which proves his fears of them watching him were very much true.
They made appearances in all seasons but Season 1, they appeared in Aelita's visions in season 2 (production wise), but Aelita's vision was chronologically before season 1. They also made an appearance in Season 3 when they came after Jeremie because XANA framed him for hacking in to the men in black's systems, and finally they made their last appearance in Season 4 when XANA created one from a polymorphic spectre to capture Aelita in town.
They may have been inspired by the agents in Men in Black, the Matrix trilogy, or in the real world, from the United States Secret Service.