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While docked at Peirpont Drift, a cop recognizes Beka and Seamus and notes that they are wanted for various crimes, but for some reason does not arrest them. Meanwhile, Dylan tries to mediate a disagreement between the Than and an ally of the Free Trade Alliance.

While attempting to get the Arazians to rejoin the Commonwealth, he is arrested for sedition and sentenced to life imprisonment. In prison, he is forced to defeat a Magog prisoner in battle to win his share of the food. He wins the respect of the woman who appears to be in charge and finds Romy caged. Meanwhile, the crew of the Andromeda is anxious to find their captain.

Captain Dylan Hunt attempts to drive the invaders from his ship. He manages to scare Gerentex off, but he leaves many of his employees behind. He takes the Maru and uses it to send the Andromeda, still without engine power, on a course back into the black hole. The remaining scavengers work with Dylan to regain engine control and break free from the gravity well. Once free, they regain control of the Maru from Gerentex and Dylan invites the survivors to join his crew and reestablish the Commonwealth.

When a long lost love returns, Tyr disappears from the ship to protect her from an assassin.

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.

The Sabra-Jaguar pride goes to war with the Drago-Kazov, pulling Dylan and the Andromeda along with them, as per the terms of the Commonwealth treaty. Harper receives a message from a friend on Earth pledging his support for driving the Drago-Kazov clan off of Earth. Harper attempts to get the crew of the Andromeda to head for Earth to liberate it, but Dylan refuses to take the Andromeda to Earth. Instead, Harper takes the Maru with Rommie in tow to help with the resistance.

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.

Andromeda receives a distress call from a Commonwealth prison, experiencing a riot the likes of which they've never dealt with before. Rommie discovers a now-missing prisoner was not recorded in the logs, meaning they was a mole, and Dylan and the others go in search of them.

Dylan and the Andromeda are ordered by the reformed High Guard to transport and protect a candidate for election to Second Triumvir in the New Commonwealth. To the crew's surprise the candidate is none other than Beka's "Uncle" Sid, a sneaky and sleazy "businessman" who used to work with her father. Both Beka and Dylan are concerned that Sid may become part of the ruling body of the New Commonwealth, but when they find Sid unconscious and bleeding in his office they are forced to protect him from his assailants.

Tyr leaves the Andromeda while it is in dry-dock for repairs to seek out other survivors of his pride. Dylan and the rest of the crew remain to see off the newest Commonwealth battleship, the Resolution of Hector. The AI to be installed in the Hector was derived from Andromeda and the former AI of the Wrath of Achilles, who was destroyed in a prior mission. Matters become complicated when Romy leads a strike force to take control of the Resolution of Hector.

The Andromeda gets caught in the middle of a battle between two Nietzschean prides, one of which is the Drago-Kazov. They manage to capture a hostile fighter from the unknown pride. He reveals that the Drago-Kazov believe that his pride has in its possession a legendary Nietzschean slip-scout, the Midnight's Voice, claimed to have mapped billions of transit points in the slipstream, as well as the slipstream itself. Dylan looks into the near-mythic tale of the Midnight's Voice while Tyr interrogates their Nietzschean captive.

The beings from another universe reappear. They take Rommie and use her for their own plans. The crew goes on a mission to rescue Rommie.

Andromeda investigates the site of a reported Nietzscheanattack on a Commonwealth battleship, but find no sign of any conflict having occurred.l. Dylan must deal with the Nietzscheans in order to uncover the truth of what happened in orbit.

While returning to Andromeda with repair parts after the Magog attack, the Maru comes under attack and crashes on an ice-covered planet. On board Andromeda, only Trance, Rommie, and Harper remain, with Harper struggling to cope knowing there's Magog larvae living in his stomach

During a solar storm, Dylan's forced to leave Beka and Harper planetside. When he manages to pick them up, he also picks up a creature which devours the Maru's electronics, They must find a way to stop the creatures before they do permanent damage to Andromeda.

After Harper's attacked by a dying Perseid, he gains a level of intelligence much greater than usual. A bounty hunter arrives for the dead Perseid, and Dylan looks into why the Persed was wanted. Unable to sleep, Harper begins to speak in various foreign languages, repair the ship, and invent new gadgets. The bounty hunter returns - to recover the information the Perseid lost.

While the Andromeda is hosting a diplomatic conference, Harper encounters a reporter who is able to remove the Magog larvae from his guts. She offers to remove them all in exchange for the information Harper previously had downloaded into his brain. A high-ranking member of the Sabra-Jaguar pride arrives at the conference unannounced to join the Commonwealth.

Andromeda receives a distress call from a freighter, and manages to get it into the docking bay, but it is venting oxygen and the bay doors are jammed open. Dylan and Tyr manage to save most of its crew from suffocation, but they all exhibit signs of brain damage. Their leader informs Dylan that they have escaped from a hellish slave world that no one has ever escaped from before.

Beka, Harper, Rhade, and Doyle are searching for Vedran treasure, and they find a door behind which is a test that might lead to great wealth, Rhade and Beka are trapped within, as Harper and Doyle try to free them. Dylan goes in search of Trance, who's been trying to uncover more of her lost memories.

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 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.

The governing body of the Commonwealth has voted "no-confidence" in triumvir Tri-Jema, she sends Dylan to get the Andromeda refitted and visit an augur, who is told to be infallible. This augur, dubbed Citizen Eight, aims to take Tri-Jema's place as triumvir and, according to the triumvir, remove Dylan from command of the Andromeda. The robots sent to the Andromeda to start pre-upgrade repairs turn against the crew, forcing Dylan and Harper to shut them down. Dylan must deal with Citizen Eight before he can bring down the Commonwealth from within.

A newly colonized planet of the Commonwealth comes under attack by Pyrian "pyroformers", but when Dylan destroys the machines, the Pyrian fleet arrives to defend its property. Dylan hopes to talk them out of their goals, but they are not deterred. Dylan is forced into a battle he did not want, one where he is outmatched.

Trance mourns the loss of her relative, Mesmer, but in the middle of the ceremony the Andromeda is hit by many massive shockwaves, sending the ship reeling. They discover that the shockwaves emanated from a star going supernova, and signs point towards the use of a weapon similar to a nova bomb. The crew comes to the conclusion that Marduk, a rogue planet, is the source of the weapon, but the Andromeda needs help to achieve its goals.

Harper discovers a weapon in the system which is powered by a crystal, that Harper believes will be able to restore power to Andromeda. Rhade and Dylan must go undercover working for Cutter to obtain the crystal he mines, as Andromeda and Doyle argue over who controls the ship.