The book begins with Khan, Lt. Marla McGivers, and most of the other supermen and women that had been with him on the SS
Botany Bay arriving on the planet Ceti Alpha V. Khan is given supplies and a phaser and begins to build a colony on the planet. Khan is challenged several times by his fellow supermen, but remains in control for the most part.
Six months after the supermen arrive, the next planet in the Ceti Alpha system, Ceti Alpha VI, explodes and disrupts the orbit of Ceti Alpha V. This causes major climate changes and loss of plant and animal life. Khan and the supermen take refuge underground and Khan waits for Kirk to arrive and rescue him and his followers from the hell that the planet has become.
After more time passes, several supermen do not wish to follow Khan any longer and try to assassinate Khan by placing a
Ceti Eel in Marla McGivers's ear. This bizarre creature causes her to do whatever is commanded of her, and the men order her to kill Khan. Marla's love for Khan allows her to resist enough to instead kill herself. The eel emerges from her ear after her death and Khan sees the reason why she died.
After the failed assassination, the rebels leave the underground and form a new faction on the planet, taking control of the vital hot springs that provide the only water on the planet. Khan then battles them, losing many of his followers, but winning in the end.
At the end of the novel a few years later, Khan sees two men in space suits materialize on the planet's surface.
Throughout the novel, Khan blames his hardships on James Kirk for stranding him on the planet and never checking on him again.
Secondary plot
The book also has a
frame story with James T. Kirk,
Hikaru Sulu,
Spock, and
Leonard McCoy going to Ceti Alpha V after the events of the second,
third, and
fourth Star Trek movies had already taken place. Kirk is filled with guilt and wishes to find out more about Khan's life on the planet. He leads a landing party to the bunker that is shown in the second movie. In their search, they accidentally stumble upon a sarcophagus for Marla that was built by Khan with Marla's mummified remains within. In another sarcophagus, likely meant for Khan, Spock finds data tapes and records and Khan's personal journal. This is when the book moves into Khan's story.
At certain points along the way and after Khan's story is complete, the book continues with Kirk's story. He and the rest of the party explore the underground tunnels that are beneath the bunker to learn even more about Khan's life. Before they leave, the landing party is accosted by Ericsson's daughter and a few other surviving superhumans from the second faction who were exiled from the colony, but had taken over the bunker in Khan's absence. They demand to know Khan's whereabouts, not knowing that he had left the planet and subsequently died. The young Ericsson also destroys Marla's remains with a phaser she took from the landing party. She then wants to kill Kirk, "the Abandoner", for everything that he did. Kirk manages to convince the young Ericsson that Khan was indeed dead and their fight was over. Kirk offers to take all of the supermen and women to Sycorax, a planet populated by genetically altered humans that was mentioned in the frame story of the first two novels in this trilogy. The superhumans agree to go with Kirk and say that Kirk may not be "the Abandoner" after all. Then Kirk instructs Sulu to go back to the Mutara Sector, and he then beamed Marla's ashes into the debris field created when the Genesis Planet exploded, so that she and Khan could at least be together. Kirk also hopes that as husband and wife were reunited that somewhere, somehow, Marla McGivers and Khan Singh have both finally found peace.
