An alien probe of unknown origin launches an assault on Earth; an attack so devastating that Enterprise is recalled from her voyage of exploration to help with Earth's defence. During the journey home, Captain Jonathan Archer receives intelligence that the origin of the probe is a little-known region of space called the Delphic Expanse. Vulcan Ambassador Soval informs Archer that the Delphic Expanse is notorious for bizarre occurrences, and few ships that enter it are ever seen again.

Believing there will be a second attack, Archer convinces Starfleet to let him take Enterprise into the Delphic Expanse to seek out this mysterious new enemy. In doing so, he will be going against the Suliban, the Klingons, and the Vulcans, who are removing T'Pol from the Enterprise as a result. What is more, he will have to deal with a cadre of battle-hardened marines and their no-nonsense colonel who have been assigned to his ship.