Seamus Harper pushes a pod containing the body of Gaheris Rhade before Captain Dylan Hunt. Rhade betrayed Dylan in the past, moments before the Andromeda got stuck on the edge of a black hole for 300 years. Dylan notices a scar on Rhade's hand that he had never noticed during their long friendship.

Suddenly, the crew is sent back in time, where Rhade is about to destroy Harper’s tesseract machine in an effort to stop distortions in time and space. Gold Trance and Beka appear before him. Trance tells Rhade that he shouldn't damage the machine. When he is not convinced, Trance urges him to remember the past and how time has led up this point.

Rhade remembers back to the Nieztschean ambush at Hephaestus, during which he turned against Dylan and killed him. As Rhade prepares to dispose of his body, Andromeda informs him that they are going into the black hole. The Andromeda then becomes frozen in time on the edge of the black hole.

Three hundred years later, the Eureka Maru pulls the Andromeda free. As Rhade wakes up, he finds that the ship is being boarded. Andromeda refuses to acknowledge his commands. However, Rhade does promise her that if the people boarding the ship are from the Commonwealth, he will surrender.

Rhade finds Harper, who informs him that there is no more Commonwealth, and that the Nietzscheans also did not win the war begun at Hephaestus. Realizing that he killed his friend for nothing, Rhade recruits Trance Gemini, Beka Valentine, Harper, Rev Bem, and Tyr Anasazi for a mission to restore the Commonwealth.

Unexpectedly, Trance enters the Slipstream and brings the ship to the Witchhead nebula. The Renewed Valour, a Commonwealth ship, arrives shortly after. Rhade decides to maintain radio silence but views the message that Captain Yezgar sends. Rhade discovers that they have gone back in time to just twenty-four hours before the battle of Witchhead, the final battle between the Commonwealth and the Nietzscheans.

Rhade decides that they should do nothing and Slipstream back to their own time. However, as they are about to leave, a Nieztschean fleet three times the size of the fleet from the original battle comes into the system.

While contemplating what to do, Rhade plays a game of Go with a holographic version of Dylan. The hologram advises Rhade to use one of Harper's devices to destroy a huge part of the Nietzschean fleet.

Though wanting no more death on his hands than need be, Rhade destroys the ships in order to save more lives in the long run.

Tyr is upset with Rhade’s decision, saying that he betrayed his own people. But Rhade believes that the Nietzscheans shouldn’t prey on the weak and kill for sport. While Rhade plays another Go game with holographic Dylan, they talk about how he has been unsuccessful in renewing the Commonwealth. Rhade doesn’t understand how the Maggog threat isn't enough to unite the worlds together.

Charlemagne Bolivar has been convincing potential worlds not to sign on because Rhade will not let any Nieztscheans into the commonwealth. However, he lets Tyr stay on board to keep him under surveillance. Dylan mentions the fact that Tyr has precious artifacts on board, which makes Andromeda more of a target.

Rhade calls Beka to talk about Tyr. She tells him that she can't do anything, and that things have not worked out as she expected. She decides to leave the ship.

Soon after, Rhade goes to the storage area and finds Tyr bent over the body of Drago Museveni. Tyr throws a shurican, trying to discourage Rhade, but Rhade deflects it easily with his hand Ñ though the defensive move has left a scar. Rhade then increases the gravity beneath Tyr's feet and shoots him dead with his force lance.

Meanwhile, Maggog eggs implanted in Harper on a previous mission begin to hatch. Harper plans to build a tesseract machine, which can fold time and space, in order to remove the eggs. Harper requests that the ship go to Sinti so that he can ask the Perseids for help building the machine. Beka returns to help Harper and be with him.

While the machine is under construction, it creates time and space distortions that affect nearby Sinti. Harper tells Rhade that the distortions are coming from the time it was built, in the future.

Meanwhile, on the Eureka Maru, Beka fights off Kalderans while Purple Trance meets Gold Trance. Wanting a good future, the two Trances switch places.

Finally, Rhade finds the machine and prepares to destroy it. But just as he is about to shoot, Beka and Gold Trance appear before him. Trance informs him that Dylan is the one to reunite the commonwealth, not Rhade. To convince him, she predicts that Hohne, one of the Perseids working with Harper, will die in a few moments.

Rhade is not convinced, but decides to trust her after he is informed by Andromeda that Hohne has died.

Trance takes him back to the beginning, at Hephaestus, and leaves him to his destiny. Rhade sees himself, in the past, passing through the corridor on his way to kill Dylan. Knowing that this is not the right future, Rhade kills his past self and dons his uniform.

As he walks onto the command deck, Rhade fires at Dylan and misses. Dylan fires back, killing Rhade. At that moment, the timeline returns to normal and Dylan is back with Harper, standing over his best friend's body.

Harper does not like Rhade for what he did, but Dylan tells him not to judge. He would like to think that Rhade had the best intentions.