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.

The mysterious Man in Black kidnaps Hynek, which sends Quinn on a mission with the CIA to follow him and rescue Hynek.

Strange interlopers in the sky and sea, and the actions of a rogue admiral, threaten to turn a naval exercise into World War III. It's up to Hynek and Quinn to stop the rogue admiral.