Dylan finds himself on Seefra-1, one of nine identical planets orbiting two suns. He soon encounters Rhade, who has abandoned all hope. Rhade hates Dylan for the hope he has brought, and when someone asks Dylan be killed, Rhade agrees to do it.
Dylan and Rhade receive a month-old distress signal from Beka. After following the coordinates she left, they find the Andromeda dead in space. On board, he finds Darregacorp engineers trying to salvage it, led by Jonah Derrega, and Beka Valentine.
When a valuable painting gets stolen after Beka, Rhade, and everyone else in the bar inhales a mysterious mist, Dylan jumps at the opportunity to win the reward for reclaiming it so the Andromeda can be repaired. After tracing the nanobots in the mist, they encounter Harper who is accompanied by a beautiful woman named Doyle. But Harper is caught up in the plans of Marika, who wants him to genetically engineer Vedrans, as well as to take over the Seefra system.
When a slipstream event is detected in the Seefra system, Dylan, Rhade, and Beka try to find it, and their way out. Meanwhile, a man claiming to be from the future approaches Doyle, addressing her as Andromeda.
Beka learns she has existed in more than one place at one time when she meets a man who she knows is her father.
Dylan encounters Celine, a woman from his past and is trapped in time loops. The two are happy to see each other, but Dylan knows he may have to choose between Celine and the survival of Seefra.
The unexpected return of Flavin takes Dylan on a journey through time, revealing mysteries surrounding Tarn Vedra, the Paradine, the battle with the Worldship, and Trance.
Dylan and Rhade attempt to infiltrate a mining camp where crystals are extracted, which contain the power needed to restore the Andromeda and leave the Seefra system.
When Trance believes Rhade and the crew blame her for their situation, she runs off into Seefra-1's underground tunnels. As Dylan and Doyle pursue her, they discover the use of ancient Vedran technology.
The crew is tormented by a mysterious stranger who accuses them of murder.
An old friend who Harper thought was dead returns to help the crew in a battle for Seefra-5.
A deadly enemy from the past returns with plans to create an elite warrior race.
When Trance becomes attracted to a mysterious young man from her past, the reunion causes her to begin regaining her memories.
The arrival of Trance's sun threatens to destroy all the planets except Seefra-1 unless the system problem is fixed.
The avatar of the black hole, that trapped Dylan after the Nietzschean ambush, returns to get him back.
The crew travels to the core of Seefra's sun Methus-2 to repair it.
An explosion sends Dylan into an inter-dimensional loop, with a man named Elysian telling him to decipher a riddle.
As Trance's sun closes on Seefra-9, Rommie is rebuilt by Doyle to help evacuate the planet.
The evacuation of Seefra-5 is at risk when a religious sect decides to stay on the planet.
As General Burma arrives on Andromeda, with Harper in tow, Dylan and Rhade head for Methis 2, about to be crushed by Trance's sun, leaving Doyle, Rommie, and Beka to face Burma, and the forgotten enemy he brings with him.
With the help of the avatars of the nebula, the Andromeda goes through the Route of Ages, back to the Known Worlds, and the Commonwealth.
As the Nietzschean fleet approaches, the Andromeda prepares for the final battle.