Hynek and Quinn investigate reports of a soldier who was allegedly taken inside a flying saucer at a remote military base in Nevada, where they subsequently learn about the several reasons why the secrets contained in Area 51 should not be released.

A supposed alien invades a rural home in Kentucky, which prompts the CIA to give Hynek and Quinn access to their top-secret program known as MK Ultra, which asserts that the alien attack has the potential to be the beginning of a larger plan.

When sensitive material is stolen from Generals Harding and Valentine, Hynek and Quinn realize that their culprit is far closer to home than they could imagine, but so is undeniable evidence of a UFO conspiracy.