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.
Dylan and Rommie go into the Magog World ship to rescue Tyr, Harper and Rev. He orders Beka to use the Nova Bomb to destroy the world ship in a few hours, even if it means he and the rest of the crew will be killed.
Under attack from Nietzscheans, the Maru, bearing parts for the repair of the Andromeda, crash lands on an arctic planet. With the Andromeda still out of order, Harper struggles to cope with the Magog larvae living in his stomach while performing his normal duties.
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.
A planet asks the Andromeda for help when its cargo vessels are attacked by unknown vessels. Trance goes down to the planet to find out more about the people, and ends up being interrogated about her past.
Harper, Rev, Tyr wait for Rommie in the Maru. Rommie's on a mission to find out about a new weapon being developed. Once their contact find out she's an AI, he becomes wary of Rommie. The AIs on the planet had revolted against their creators years ago.
In an effort to allow the Andromeda, and the unarmed fleet she is escorting, to pass through a Drago-Kazov controlled system, Dylan and Tyr assault a base controlling old High Guard turrets along the route. Along the way, one of the ships in the convoy gets lost, so Beka takes the Maru to find the lost sheep.
The crew gets news of a colony that was formed when Dylan's Fiancee' escaped the fall of the Commonwealth. The colony has flourished. They have heard of the new Commonwealth. Some want to join, others feel they shouldn't. Some are willing to do anything to swing the vote their way.
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.