The Commonwealth vessel Andromeda, captained by Dylan Hunt, responds to an urgent distress call to find itself lured into a trap. Nietzschean warships surround them and open fire. Captain Hunt, in a last ditch effort, evacuates the ship and maneuvers toward a nearby black hole. Hunt's first officer, Rhade, a Nietzschean himself, betrays Hunt and attempts to kill him, but Hunt perseveres, killing Rhade in the process. Time dilation near the black hole slows time for the Andromeda and Dylan until a freighter tows it out 300 years later. Dylan now must fight off the band...
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.
The crew find an old Highguard Space Station inhabited by the teen aged decedents of the original crew. The want to rebuild the Commonwealth, by destroying opposing forces, and they have the nova bombs to do it. Andromeda's crew must show them what the real Commonwealth is about. Harper finishes building Rommie, the Andromeda's Avatar.
The Andromeda tries to help in a conflict between the Than and a Nietchean pride. Tyr, the last of his pride is offered a chance to join with the pride and a bride. Will he side with his people or with the Andromeda.
Trance tries to pilot the Andromeda through slipstream, and the crew ends up traveling back in time, to the time just before the Commonwealth fell. The crew must decide whether to take actions that could endanger the future.
Answering a distress call from a Wayist vessel, Beka is surprised to find her brother aboard. Most of the crew seem suspicious of the pair of newcomers, most of all Rafe Valentine, given his sleazy history. When he steals the Maru to visit a monastery, Beka's warnings seem to be true. However, when she finds him at a Wayist monastery, she believes that he really has turned a new leaf.
When Andromeda runs experiments on a black hole, Dylan sends a message into the black hole saying goodbye to his loved ones. The message is received by the woman he left behind, 300 years earlier, a side affect of the experiment. When they find a way to transport him back to that time, he knows he cannot stay and prevent the fall of the Commonwealth. But can he bring his fiancée with him to his new time?
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.
A chancellor visits the Andromeda, Tyr disrupts his visit by bringing up some past deeds the chancellor committed against Nietzscheans. Dylan orders Tyr to apologize, as Tyr visits the chancellor, the chancellor is killed and Try is found unconscious. Andromeda's crew must find the culprit.
Upon nearing El Dorado Station, Beka receives a message from her "Uncle Sid", who seems to be be in urgent trouble. She goes to meet him, with Trance in tow; meanwhile, the men on Andromeda attempt to sell what they don't need in order to buy new parts. Beka finds Sid calling himself "Sam Proffit" and running TransGalactic, one of the largest shipping companies in the galaxy.
While Trance has taken an unannounced vacation, Dylan and the rest of the crew investigate the remains of a derelict High Guard starship, the Pax Magellanic. There they find the last of the crew over 300 years old, but seemingly unaffected by age. They claim that it is due to radiation from the destroyed planet nearby and since their slipstream drive was irreparably damaged, they have remained in the asteroid ruins of the planet.
After Harper is 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 he was a wanted man. Unable to sleep, he begins to learn foreign languages, repair the ship, and invent new gadgets. The bounty hunter returns to recover the information the Perseid lost.
A mission Dylan performed for the old common wealth comes to haunt him. He and his partner deposed a tyrannical despot on Mobius. His replacement turned out much worse, a person Dylan inadvertently put into power. The replacement is still alive. Now Dylan must eliminate his replacement, or is there another way?
When the Andromeda passes through a debris field, the crew is surprised to find the debris forces its way into the ship and forms an android, who claims to come in peace, expecting a hug. He claims to represent the Consensus of Parts, a mythical mechanical culture from uncharted regions of space, and wishes to take the Andromeda to the "directing intelligence", which seems to be his superior. In an effort to gain a new ally for the New Commonwealth Dylan decides to make contact with the Consensus.
While Trance and Harper are out on the Maru, they are surprised to find Gerentex aboard. He forces them into helping him resolve his debts. Harper manages to turn the tables on Gerentex and learns about his new scheme.
Dylan and Rev respond to a request for aid from Rev's former master. There Dylan prepares them for defending themselves against the bandits in the event that the Andromeda does not show up to scare them away. Rev's master is concerned about the effect that teaching them to kill will have on their children, as these humans have a genetic memory, passing down their memories to their children at birth.
The Andromeda attempts to defend a freighter from a Restorian fighter, but in its last moments the fighter rams the freighter, destroying it and all 536 aboard. However unlikely, one escape pod escaped the explosion carrying a humanoid android named Gabriel, who claims to be a teacher fleeing from his oppressors. An admiral representing the Free Trade Alliance arrives offering information on the Restorian flagship, a refurbished Commonwealth destroyer. Dylan puts a plan into motion to destroy the flagship, while Andromeda's avatar develops a relationship with Gabriel.
Harper overrides some of Andromeda's protocols to fake a reactor meltdown to spring a surprise party for Dylan on his birthday. Beka gives him a unique gift, the map to Tarn-Vedra, the Commonwealth capital of legend. There is anxiety among the crew as they prepare to begin their journey. Seamus and Beka share an interest in an item they believe to be located on the Vedran homeworld.