(This episode incoporates a series of flashbacks. Paragraphs in italics are flashbacks.

Beka and Tyr are on the Andromeda, working out, while waiting for the rest of the crew to return from a parts run. Beka is particularly worried about the fact that Dylan took both the Maru – not just her ship, but her home and source of income for many years – and Trance, who she considers her "lucky charm".

On the Maru, Dylan sends a message to Rev and Harper (who are looking for the required parts elsewhere) that he has found the parts. Suddenly, he is attacked by unknown assailants, who knock him out and drag him off, but not before he rips a button off one of the attacker's shirts.

Trance returns to the Maru, notices Dylan is missing, and finds the button.

Dylan is being interrogated, accused of murder, terrorism, and conspiracy. He only gives his name, rank, and serial number, so his interrogators resort to torture.

Admiral Stark, Sara Riley's (Dylan's fiancée) aunt, offers an undercover, voluntary mission to Dylan. She emphasizes the number of lives at risk (5 billion), and assures Dylan that, if the job is done right, no one will have to die. Based on this, Dylan accepts. She introduces him to his partner on the mission – Gaheris Rhade.

Trance uses the Maru computer to identify the pattern on the button, sends a message to Rev and Harper asking for help, and goes in search of Dylan.

Dylan's interrogators accuse him of planning the assassination of their leader and overthrow of their government. Dylan denies this, but is surprised when he is introduced to the leader in question, and it is a familiar face.

The mission that Dylan has volunteered for is to kidnap/extradite Ferrin, the Chancellor of the planet Mobius, which has been attacking a neighbouring world. Neither Mobius nor the neighbouring world are members of the Commonwealth, but Admiral Stark insists that it is important for the sake of peace in that sector of the galaxy. On Mobius, Dylan and Rhade meet their contact, Ferrin's architect – and the same man that has just been introduced to Dylan as the "Great Compass", the current leader of Mobius.

Rhade feels that killing Ferrin would be a successful completion to their mission, but Dylan insists that their mission is non-violent.

After the completion of the earlier mission, Venetri (the "Great Compass") researched Dylan's identity. He heard of the attempts to restore the Commonwealth, and that Dylan was behind it, in connection with the death of President Lee on Castalia. Based on this, and the previous mission, he has come to the conclusion that assassinating leaders is Dylan's standard procedure.

Venetri tells Dylan and Rhade that they are "already farther than the others". Dylan is surprised to hear that there have been previous missions – Venetri tells him there have been about a dozen attempts. Venetri just wanted to build things, but Ferrin went "over the edge". Rhade sees this as further proof that killing Ferrin is an acceptable option.

Tyr is reading Nietzsche, but Beka is restless. They discuss the basics of Nietzschean philosophy, and Tyr says that he respects Beka's survival instinct.

Dylan, Rhade, and Venetri come across a guard. Venetri tries to bribe him, but a second guard interrupts, and attacks them. Dylan and Rhade kill the guards.

Dylan is presented with a video of himself killing the guard, only with Venetri edited out of the picture. Based on this evidence, Dylan is accused of murder. The interrogator identifies herself as a descendant of the guard Dylan killed. She says that his children suffered in a refugee camp, until they were rescued by the Great Compass. Dylan is dragged off and subjected to a mock execution, but he still offers no more than his name, rank, and serial number.

Venetri panics about the killings. Dylan accepts that killing is always a possibility in the course of a soldier's job, but insists that he had good intentions, they just made a mistake. Rhade doesn't consider it a "mistake", because they are still alive.

Trance locates Dylan in his cell. When he asks how she found him, she says it was easy – she had the button. She says that she used to "find things" for people and "take them". Dylan asks if she was a thief, but she says she was not, because she never had bad intentions.

While Rhade speaks of his admiration for Ferrin's efficiency, an alarm goes off. Dylan suggests that the best way to guarantee their safety is to obtain an important hostage – Ferrin.

Trance says that she is going to get Dylan out, but Dylan realizes that he started something wrong during his previous mission, and he feels responsible for making it right.

On the Andromeda, Tyr and Beka are manually performing maintenance tasks while they are waiting for the parts. To relieve the boredom, Tyr offers to make a gourmet dinner for them – he learned to cook for a previous employer.

Dylan and Trance find Venetri's "clone lab" – he has stayed alive for 300 years by making clones for "spare parts". Dylan decides that he has to be stopped. Thinking over what Trance has done, he asks her if she can see the future. She says that she cannot see "the future", as such, but she can see possibilities. Dylan asks her which way they should go, but the way she picks turns out to be a bad choice – they run into some guards. They manage to incapacitate the guards, and Trance chooses a different direction.

Beka asks Tyr if he thinks there is a shipboard romance happening. Tyr interprets that as implying the two of them, but Beka claims she meant Dylan and Rommie. Tyr asks what the point of that relationship would be, since they're not the same species. Beka asks if that means that Tyr (a Nietzschean) would never be interested in a human woman. Tyr says he never would. Beka, insulted, walks out on him.

Dylan and Rhade force their way into Ferrin's office, but Ferrin pulls a gun and fires at them. He wounds Dylan, but Rhade and Dylan shoot and kill him.

Dylan concludes that Rhade was right – the best/only solution is violence, but Trance stops him, and reminds him that there are other possibilities. He cannot control the future, but he can control his intentions, and maybe that is enough. Dylan accepts her advice – he goes into Venetri's office with his gun drawn, but does not open fire. Venetri claims that the gun proves Dylan's bad intentions. Dylan claims that the first time was a mistake, but Venetri claims it gave him what he wanted.

Stark debriefs Dylan and Rhade. While the outcome of the mission was not ideal, it was acceptable to the High Guard. As a result, she assigns Dylan and Rhade to the Andromeda – Dylan as captain, and Rhade as first officer. Dylan tries to turn it down, because he feels he failed on his mission, but Stark tells him this mission is not voluntary.

Trance reminds Dylan that despite how he may have got the Andromeda, he has used it for good.

Dylan tells Venetri that he wants justice and freedom for Mobius, and he is not going to kill him. Trance suggests a system that needs architects. Venetri is surprised that they are going to "just let him go", but Dylan says that they need to break the cycle of violence on Mobius. Venetri says that he is willing to turn power over to the senate to arrange popular elections.

Beka and Tyr are once again performing maintenance tasks manually, and the tension between them is apparent. As they finish, Dylan returns with the parts, and the repairs are made.