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XCOM discovers the high likelihood of an Alien Base hidden somewhere on Earth after capturing an Outsider Shard. After studying the shard, XCOM is able to identify a communication frequency that allows them locate the underground base; the Alien Base is located on a random continent for each game.
In addition to serving as a command and control center and supply depot for the invaders, the Aliens have been transferring abducted humans here to experiment on them.