Trance has taken off on an unscheduled side trip. Dylan is frustrated by the number of "unauthorized vacations" being taken by the crew – he considers it "going AWOL". Beka tells them that that is how they did things on the Maru, they are not a military crew.

In his quarters, Dylan talks to Rommie – he says he needs to remember that the crew signed on for the comfort and security of living on the ship, not for his quest to restore the Commonwealth. Beka enters, and presents Dylan with a "peace offering": A flexi with information that Gerentex had gathered about another possible surviving High Guard ship.

Harper claims that this ship is a "ghost ship", and he does not want to go. The legend is that it "glitters gold", and that no one who sees it comes back alive.

They head to the Herodotus system in search of the ship. Therein, they find an asteroid belt, although there is none on their chart. They also begin to receive a voice transmission, which is repeating the words "no tears" in an eerie voice. Searching through the asteroids, they find a gold-coloured High Guard cruiser, the Pax Magellanic, a sister-ship of Andromeda's.

Dylan, Rommie, Beka, and Harper board the Pax Magellanic on the Maru. The Pax's internal defenses begin to fire at them, but Dylan deactivates them with his High Guard security code. They are then greeted by Lieutenant Jill Pearce and other members of the Pax's crew. According to Jill, they are, in fact, the original crew, who have somehow survived 300 years. Jill postulates that it may be a side effect of whatever weapon the Nietzscheans used to blow up the planet. She tells Dylan that Captain Warrick is dead, and she is the senior surviving officer.

Jill and Dylan compare notes about their High Guard training. They remember many of the same places on Tarn Vedra. Jill also tells Dylan how the battle was going badly, and the Nietzscheans blew up the planet. Their slipstream drive was also irreparably damaged, and, since it would take them many years to get to the nearest system at sublight speeds (their current maximum is 10 PSL), and they do not know if they will start aging again when they leave the system, they decided to stay and wait for help.

Rommie is unable to interact with the ship's AI by normal means, so she attempts to access it via the ship's VR matrix. If she cannot do this, they may have to erase it.

Dylan is clearly enjoying the return to military protocol and discipline on the Pax, while Beka is mostly just amused.

Dylan and Jill arrange to have dinner together to discuss the situation. Dylan hopes to convince her to join him in restoring the Commonwealth.

Rommie enters the VR matrix, to find the ship's avatar. It is featureless, and repeating phrases like "Can silicon cry? Can computers weep?" It does not allow her to access the data, even with her security codes. She eventually manages to see some visual records from the day of the battle. She sees Warrick taking troops to the planet, but he orders Jill to stay behind. Rommie is then forced out of the VR matrix. Rommie reports this to Dylan, and he tells her to keep trying.

Rev has analyzed the cells of the crew of the Pax, and determined that they are, indeed, 300 years old – but the crew of the Andromeda has continued to age normally since they arrived. Beka is suspicious.

Tyr reminds Dylan that Nietzscheans do not, generally, destroy habitable worlds, especially ones they are currently on. He has analyzed the debris, and is of the opinion that the planet was not destroyed by a Nietzschean weapon, nor was it destroyed by natural causes. He does not say it, but he implies that he believes the Commonwealth destroyed the planet.

Harper and Dutch, the Pax's engineer, work on getting into the slipstream core, which has been welded shut.

Beka and Rommie head back to the Pax on the Maru. Rommie is concerned about the ship's AI. Beka understands her concerns, because the Pax is like family to Rommie, and Beka has the history with her father. She tells Rommie that sometimes you have to accept that there is nothing you can do to help.

In the VR matrix again, Rommie sees more of the day of the battle. She sees the ship, empty except for Jill on the bridge. Warrick is giving her an order (over the radio) that she does not like.

Dylan and Jill talk over dinner. Jill spent the past 300 years in various pursuits, including studying Earth opera. She currently has "Der Fliegen der Hollander" (Wagner's "The Flying Dutchmen") playing, and relates some of the story to Dylan. She relates to the mariner doomed to sail the seas forever without purpose. Dylan vows to help her re-discover her purpose. He is reminiscing about Tarn Vedra when Rommie returns.

Rommie states that Jill was responsible for destroying the planet and killing Warrick. Jill admits that she did it – Warrick's position was overrun, General Skyfalls was dead, and he called down friendly fire to avoid capture. She speculates that the kinetic missiles sparked a chain reaction that destroyed the planet. Dylan reassures her that she was following orders, she should not feel responsible. Rommie asks her why she did not tell them earlier. Jill says that it was a painful memory – perhaps she was repressing it. Rommie thinks she can use the information to help the AI. Dylan and Jill discuss her "survivor's guilt".

Harper and Dutch have managed to get to the slipstream core, to find it missing. Dutch suddenly attacks Harper, and attempts to throw him off the catwalk. Beka comes to Harper's rescue. They get away, but the rest of the Pax's crew start attacking them as well. They shoot some of the attackers, but they get right back up again.

Rommie is back in the VR matrix, and the AI is resisting her attempts to find out more.

Harper and Beka interrupt Dylan's dinner to warn him that the crew members are all androids. Harper triggers a diagnostic program which shuts them all – including Jill – down temporarily. They run for the Maru, to get Rommie out of the VR matrix, as the androids start to re-activate and resume the attack. They get Rommie out of the VR matrix and attempt to leave, but the hangar doors will not open.

Dylan realizes that Jill is, in fact, the ship's avatar (Ma-Jill-anic), and controlling the androids. Rommie says that she has changed her avatar – the one she knew was called "Maggie". Tyr says that they must erase the AI, and Dylan starts the process, but Rommie stops him. She says that Jill is a person, and deserves due process.

Dylan and Rommie go into the VR matrix together, to try to fix the situation. The featureless avatar becomes Jill, and cooperates with them. She claims that Warrick "tried to kill her" – he had ordered her to self-destruct. She replays the records, showing Warrick giving the order. Jill says that they "can escape", but Warrick re-states his order. Through the course of examining the records, it becomes apparent that Warrick had initiated a romantic relationship with Jill. Ultimately, Jill refused Warrick's order to self-destruct, ejected the slipstream core, and destroyed the planet. She then used the ship's DNA files to make androids of her favourite crew members. Dylan states that Jill betrayed her High Guard oath. Jill attempts to attack them with a power surge, but they get out in time.

The androids manage to force their way onto the Maru, but Tyr comes to the rescue, shooting down the androids one by one.

As Dylan, Beka, Rommie, Tyr, and Harper return to the Andromeda, the Pax starts firing. Dylan orders them to fire, but only to disable the weapons, not destroy the ship. Tyr fires a missile barrage, but the Pax explodes – she let down her defenses. Jill, on the view screen, tells Dylan how the story of the Flying Dutchman ends: The Captain's lover kills herself, hoping to find peace.

Beka tells Dylan that she understands why he likes the protocol and discipline of a military crew. Dylan tells her that he has what is important – a crew he can count on.

Rev tries to help Rommie deal with the loss of her "sister". She asks him if he thinks AI's have souls. Rev says that he thinks that anything that can love has a soul.