Dylan finds Harper, he's not happy to see his former Boss. He's adjusted to life on Seefra. Soon he'll need Dylan's help to help him out of some trouble with one of his project. Dylan also finds another member of his crew.
Doyle is plagued by nightmares, and half remembered dreams of life on board the Andromeda. But she was never a member of the crew. One person notices her perceptions are off and realizes Doyle doesn't know who she really is and tries to get her to join with him and others of their own kind. Doyle will learn the truth of her origin, and why she feels at home on the Andromeda.
Beka receives a message from Virgil Vox, the radio personality, concerning a secret from her past. She follows his instructions to a secluded community, where she impersonates a dead child, who would be about her age now. Her "father" reveals that he has been guarding a secret and that it is now time for him to pass it on to her.
A new woman arrives in town seeking Dylan's aid. She reveals that she was a Commonwealth scientist before it fell and that she is trapped in a time loop. Dylan attempts to save her from her fate and decipher the code that will restore Seefra to its proper alignment.
The return of Flavin sparks a conflict between two rival gangs over who gets his ship and the bounties within. Rhade and Harper play the two sides to make money off their enmity. Meanwhile Flavin leads Dylan on a journey to help him develop as a Paradine.
Harper discovers a new weapon in the system that is powered by a crystal, which Harper feels will be able to power the Andromeda. Rhade and Dylan must go undercover working for Cutter to obtain the crystal he mines. Meanwhile, Andromeda and Doyle conflict over who controls the ship.
A bar fight spills out into the streets and a remark from Rhade aimed at Dylan drives Trance over the edge, causing her to leave the Andromeda. While she is in the underground tunnels, she befriends a sweeper, who believes she is a princess and wields a weapon that turns enemies to stone.
Rhade, Harper, and Beka each have some dealings with the "Stranger", he is shortly murdered. Now they're all on trial for his death. The guilty party will be killed at the end of the trial, but there's more to this trial than they suspect.
While Rhade are busy defending refugees on Seefra Five from the army of a local warlord, Dylan is surprised to find Hohne, the Perseid scientist lost and assumed dead during the problems with Haprer's tesseract machine, tesseract onto the command deck of the Andromeda. Hohne and Harper attempt to recreate the quantum teleporter in order to resupply the pinned-down refugees and during the reconstruction receive a message from the research station near the black hole where the device first worked.
Beka's new boyfriend turns out to be more than she suspected. He will play an important role in the development of the original CommonWealth. Beka learns a secret that should help them if they can ever escape from Seefra.
Beka, Harper, Rhade, and Doyle are searching for Vedran treasure. They find a door that is rumored to hold inside a test that if passed will yield great wealth, but if failed will cause madness. Rhade opens the door and follows Beka inside, but Harper and Doyle are left behind as the door shuts behind the pair. Trance teleports to a carnival on Seefra Two to attempt to uncover more of her lost memories. Dylan goes in search of her, while Harper and Doyle attempt to free Beka and Rhade.
Harper discovers a program built into the Seefra system that can destroy eight of the planets, likely as a defense mechanism. Dylan begins plans to evacuate the eight planets, but is interrupted by a new arrival through the Route of Ages. The rest of Trance has returned to remake Tarn-Vedra, but the mechanism designed to that is not working.
While Harper develops a way to save the Seefra system from its impending doom, a spy has slipped on board the Andromeda. Dylan, Rhade, and Trance all feel that someone who should not be aboard is, but cannot confirm their suspicions. Things turn south when the spy attacks Beka by opening a portal to open space inside the ship.
When the blinking sun of the Seefra system goes dark for an extended period of time Dylan takes the opportunity to study the workings of the artifice in the hopes of finding a way of fixing the broken sun. Harper discovers a maintenance protocol built into the sun by the Vedrans that will allow a further extended period of time to study the sun.
Dylan is gravely wounded in a lab accident, but wakes up in the bar with Harper telling bad jokes. He is confronted by a man who is wielding Dylan's force-lances and delivers a cryptic message. After a quick fight with Dylan, the man drops to the floor without apparent cause, but returns in the guise of Rhade to catch Dylan off guard, killing him swiftly. Dylan awakens on med-deck but finds that he has returned just after the accident and does not remember Trance.
Dylan deals with the residents of Seefra One who are unhappy with the number of refugees arriving on their planet. While Beka evacuates Seefra Five she detects a ship full of Nietzscheans headed towards the dying planet; however there have never been any Nietzscheans in the Seefra system with the exception of Rhade. Harper and Rhade find the refugees they were supposed to pick up from Seefra Five killed by their former general.
Harper has been captured by General Burma, a man who believes all technology to be evil. Dylan struggles with recovering Harper, evacuating all the remaining Seefran planets to Seefra One, a.k.a. Tarn-Vedra, and dealing with Trance. Dylan supposes that something may have happened to Trance while inside Methus-2, the artificial sun they fixed and the last place Trance seemed to be herself, and goes to investigate.
Dylan and his crew deal with the survivors on Seefra One promising them that it will soon become like Tarn-Vedra once was. Harper works on getting the "low-tech" mechanism inside the planet to work properly, while Trance explores her new powers resulting from the re-establishment of her sun. She introduces Dylan to the group that her impersonator worked for, "the Nebula," a group of stars controlling all the galaxies, also an enemy of the Abyss.
The Earth explodes before Harper makes his visit, the Andromeda manages to save Harper from destruction and runs from a Nietzschean attack fleet coming from the ruins of the planet. Analyzing fragments of the destroyed planet, Romy finds radical isotopes, proof that the Abyss aided the Nietzscheans in the destruction of Earth. Dylan consoles Harper for his loss, then prepares for the battle against the joined Nietzschean fleet, comprised of the Drago-Kazov, Mandau, and Sabra-Jaguar fleets.