In a grim alternate universe to Star Trek : The Original Series, the apocalypse is coming in the form of King Ghidorah, the three-headed monster. Worse, the creature is worshiped by the hate-filled on many Federation worlds, each of whom believes they alone will be spared when the monster comes. On Earth, they have ascended into Starfleet Command itself. The family of James T. Kirk wages a generational war to oppose this evil, but often at a high price. Among the highest are those paid by young Peter Kirk and Saavik.

Prophecy Boy meets Prophecy Girl, but all is not hugs and kisses for the Chosen Ones, and their love must conquer a bigger all than most. Kirk and the Fleet chafe under the yoke of the corrupt Admiralty Hall. The long nightmare is over, but war is in the offing.