October 5, 2140. After a half-dozen years of research and testing, Starfleet prepares to launch its first warp 5 vessel—Daedalus. Propelled by a radical new engine designed by Earth's most brilliant warp field theorist, Victor Brodesser, the new ship will at last put the stars within mankind's reach. But on the eve of her maiden voyage, a maintenance engineer, Ensign Charles Tucker III — "Trip" to his friends—discovers a flaw in Daedalus' design. When he confronts Brodesser, the scientist—as charismatic as he is brilliant—eases Trip's concerns. The ship launches on schedule, and as Trip watches in horror, it explodes in a catastrophic ion cascade reaction, killing all aboard. Thirteen years pass. Still haunted by memories of that disaster, Trip now serves as chief engineer aboard Enterprise. When a freak explosion cripples his vessel, leaving her helpless before a surprise attack, Trip is forced to abandon his ship—and his shipmates. As he is on the verge of mounting a desperate rescue attempt, however, a shocking turn of events forces him to confront the ghosts of Daedalus one final time.

Swept into an alternate universe and a deadly civil war, Archer and the crew of a crippled Enterprise are imprisoned by a brutal warlord and face subtle biochemical differences that will kill them if they remain.