The crew encounters some ships, the remainders of the Commonwealth Fleet. The leaders went into hiding when the fighting broke out. They need to find them to restore order to the Commonwealth.

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.

Dylan is sent on a mission by a triumvir, but is not well informed of the danger he faces. After a haphazard reentry from slipstream, the Andromeda is captured by a gravity field projected from the moon that is the target of their mission. Dylan discovers that the moon is the base of Kroton, a half-human, half-android genius that created the Magog world-ship. Dylan attempts to take out Kroton along with the new weapon he has developed.

The Andromeda investigates the site of a reported Nietzschean attack on a Commonwealth battleship, but find no debris and no sign that any conflict occurred there, much less the reported destruction of a High Guard vessel. Dylan is invited by the Nietzschean rulers of the planet to visit and accepts, but in his descent a solar storm hits the planet, causing his escorts to fall behind. Dylan must deal with the Nietzscheans in order to uncover the truth of what happened in orbit.

Andromeda comes between two Nietzschean siblings. One has the File D, a weapon that can eliminate higher brain functions. The other has her nephew hostage, she wants File D. The crew doesn't want either of them to have File D.

Tyr returns and he's sided with the Collectors against his former crew. He wants the map for the Route of Ages.

The collectors tell Tyr why they need the map for the Route of Ages. It's a map to the Abyss, and hopefully a way to contain it. Tyr has Beka and the crew has the map. Now it's a race to the Route of Ages. Tyr makes a deal with the Abyss, and a final confrontation will ensue.

After taking a wrong turn in slipstream, the Andromeda receives a distress call from a Commonwealth prison, experiencing a riot the likes of which they have not seen before. Dylan and his crew quickly put down the rebellion, but Dylan keeps having flashbacks to the last time he was on this planet. Romy discovers that a now missing prisoner was not recorded in the logs, implying that she was a mole. Harper is shown the source of the planet's power and is told to bypass the ancient security system guarding it, so that the warden can keep it safe elsewhere. Meanwhile, ...

Harper is the key note speaker at a conference on dealing with the Magog threat. When a scientist is kidnapped, and others are killed, the crew must figure out who is responsible. Meanwhile Dylan is kidnapped by the Collectors, who make him an offer to join with them

The daughter of a King is kidnapped by a ruthless renegade. But when the crew finds her, she says her father tried to kill her, and the Renegade is actually a hero. Whose telling the truth?

Dylan and the crew are put on trial by the Commonwealth. The Collectors now control the Commonwealth. The crew wants to escape, but Dylan wants to stick out the trial, to determine if he still has ANY allies in the Commonwealth he helped to rebuild.

Andromeda captures a smuggler with a shipment of bioarmor. They try to track down the origins of the armor. But there's more to the living armor than they first realize.

When Dylan activates an experimental cloaking device, he gets swept into an alternate dimension. Harper is the commander, he has overthrown the commonwealth, and is unknowingly working for the Abyss. Dylan looks for allies to oppose Harper, and to find a way to get back to his own dimension

The Andromeda encounter 2 ships with depleted engines and weapons. They come from a planet, where the two sides have been fighting for as long as anyone can remember. One side is suffering from a disease, they claim the other side is using biological weapons, but the other side says they didn't do it. When Dylan becomes infected, the crew must figure out the source of the virus to save the captain.

Rev Bem contacts Andromeda, he knows of a weapon against the Abyss, he will only show Dylan, in person. Dylan is captured, and stranded on a warship, with no engines, and heading towards a black hole. The crew searches for him, and finds an unexpected ally in the form of a Collector.

Beka's recent behavior is explained. The Abyss has infected her, they must find a way to cure Beka, and free her of the Abyss.

Half the crew is captured. Harper works on a time bridge for the Partriarch. The other half tracks down a smuggler.

An emissary from Tri Gemma arrives, claiming that Tri Gemma is still on the crew's side, despite the current circumstances. Is she telling the truth or is she after something?

Rommie has become too emotional, the Andromeda cuts off her access and runs a full diagnostic to bring the avatar under control, this takes away many of the ship's resources. The Magagog are attacking the crew must defend Andromeda without aide from the AI. Even if they succeed in defending the ship, they may lose Rommie.

The Andromeda rescues a defenseless ship from former Commonwealth fighters. The inhabitants are an Ambassador and his pilot, returning to Arkology from successful peace negotiations with the Magog on board the World-Ship. However, the treaty is revoked when the ambassador dies from the Magog hatching in his stomach. The pilot, a Nietzschean from a supposedly extinct pride, leads the Andromeda to Arkology, a place of peacefulness in all aspects of life, to warn them of the coming Magog attack.

With the Magog World-Ship at hand, Dylan must defend Arkology as one of the Paradine, beings said to have witnessed the creation of the universe. Beka makes her decision to leave the battle while she still can. Harper and Rommie attempt to get Arkology slip-capable again before the World-Ship destroys it.

Beka decides to leave the crew to fight for themselves, but after all of the promises that everyone will be reunited, Trance tells them that they will never be as they are again. When the Magog Worldship finally re-encounters the Andromeda after two years, Rommie and Harper race to take the Arkology to slipstream, Rhade must teach the inhabitants to defend themselves, and Dylan and Trance fight off the invading Magog. But as the Andromeda becomes covered in swarmships, Trance tells Dylan that he--and only he--may escape this alive.