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The Counteroperation, also known as the Counteroperation Protocol, was a program created and overseen by the U.S. government and MTT Industries. It was created in response to the Godmodder's own Operation in Destroy the Godmodder 2. The protocol was based in the Conclave, a skyscraper in Washington D.C. The Counteroperation was, on the surface, a task set by the top computer scientists from around the globe to try and stop the Operation, though this was a front. The Protocol's real goal was the creation of an artificial intelligence known as Project Binary that would destroy the Godmodder and the Operation. Project Binary was built in Aperture Science by the facility's workers and the Advanced Superiors, hidden from the rest of the world.

Upon Project Binary's creation, the A.I. formed its own agendas, turning the Protocol into an event known as the Arrival. Binary formed an elite team of him and three other personnel - GLaDOS, King Ikea, and Bill Cipher - in order to storm the server of GodCraft themselves. Project Binary also began to manipulate the minds of nearly everyone on Earth into believing that Minecraft needed to be destroyed completely. As a result, the Counteroperation's goals shifted over time to destroying Minecraft and imprisoning all who played it, including the Descendants. Team Mojang, who had originally been a part of the Counteroperation, was exiled from the project so they could not try to undo Project Binary's work. As a result, Mojang hid underground. The Counteroperation was officially terminated upon Project Binary's death and the release of Minecraft 2.0, which restored Earth after Project Binary destroyed it in a kamikaze attack. With the threat of the Operation gone, the Conclave was torn down.

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