Following the explosive events of Star Trek: Nemesis, the Romulan Star Empire is in disarray, and Ambassador Spock attempts to render aid by launching a last-ditch effort to reunify the Romulans with their distant forebearers, the Vulcans. But when Spock is publicly assassinated at a Romulan peace rally, Starfleet and the Federation are unable to search for the criminals responsible without triggering an intergalactic war.

Thus, it falls to James T. Kirk, now retired, to investigate his beloved friend's murder. Given clandestine assistance by Captain Will Riker of the Starship Titan, and accompanied by his good friend Jean-Luc Picard, Kirk travels to Romulus as a civilian, along with his five-year-old child, Joseph, the cantankerous Doctor McCoy, retired Chief Engineer Montgomery Scott, as well as several members of Picard's crew, still waiting to return to duty on the badly damaged U.S.S. Enterprise NCC1701-E. But on Romulus' sister world, Remus, Kirk unexpectedly encounters an alluring enemy from his past as Picard and he discover Spock's apparent murder hides an even deeper mystery, reaching beyond the limits of the galaxy.

Trapped on a deadly, alien world on the eve of a Romulan civil war that could plunge the galaxy into a civilization-ending conflict, Kirk's investigation brings him to the heart of a staggering conspiracy. As he discovers the true threat facing the Romulans, he realizes that he must sacrifice the freedom of his son, whose very blood holds the secret to his destiny. Captain's Blood brings together both generations in a battle for the existence of all life in this galaxy, and beyond.