Dylan and Tyr are investigating a missing Nietzschean colony, which was attacked by the Genites. They find nothing, and are attacked by Genites. The fight is not going well for them, but a new group joins the fight, attacking the Genites and driving them back. The leader of this group, who identifies himself as "The Patriarch", and his troops as the Templars, tells Dylan that he received the same information as Dylan did, and moved against the Genites.

As Dylan arranges for the wounded Templars to be cared for on the med deck, the Patriarch explains that the Templars were founded after the fall, by Admiral Constanza Stark, Dylan's old commander, and he is Constantine Stark, her descendant. Dylan asks him where the Templars have been for the last three years, and Stark tells him that they have been working "behind the scenes".

Dylan receives a message from the Commonwealth command, telling him that they cannot officially acknowledge the Patriarch and the Templars, but, off the record, they approve of his working with them.

The Patriarch explains to Dylan that the Genites are familiar with the Templars' troops and tactics, and Dylan represents an "edge" for him in the fight.

Privately, Dylan notes, to Rommie, that the Patriarch uses a lot of the phrases that Dylan learned from Admiral Stark. While the Patriarch has given Dylan a lot of information on the Genites, Dylan is not completely sure that he can trust him or his information, since it seems too easy. Stark always told him not to trust too easily, and to verify his sources.

Dylan plans a covert reconnaissance mission to a Genite base to verify the Patriarch's information, with the Templars providing a diversion. He assigns Beka as pilot for the mission – she agrees, but wants to know what their target is. The Patriarch explains that the Genites have designed a devastating viral bio-weapon to target genetically engineered humans – which, at this point, is 92% of the human race.

Tyr is unsure of the wisdom of the mission, as he does not trust the Templars. He suggests targeting a larger Genite base in the Heimdahl system. In the course of the discussion, the Patriarch reveals that he knows a lot about Tyr, including the existence (although not the location) of Tyr's son, Tamerlaine. When Dylan tells the Patriarch that he does not intend to take Tyr along on the mission, the Patriarch is disappointed. The Patriarch also warns Dylan that he does not think that Dylan can trust Tyr, because Tyr is a Nietzschean.

Beka successfully evades detection and pilots the Maru into the Genite installation. During the flight, the Patriarch reveals that he also knows a fair bit about Dylan. On the asteroid base, Dylan and Rommie successfully hack into the Genite computer system, and locate the bio-weapon research, while the Templars engage the Genites in an extended firefight elsewhere in the complex. However, a smaller group of Genite guards corner Dylan and Rommie, who call to the Templars for support. The Templars rescue them, but one of the last Genites standing shoots and injures the Patriarch, seriously enough that Dylan feels that they cannot move him safely.

The Patriarch tells Dylan that he lost a leg in combat in AFC 263, 42 years ago, but it was re-grown by nanobots. Dylan is surprised to hear that he has been in action that long.

Tyr is left in command of the Andromeda, and takes the ship to Heimdahl. Harper protests, but Andromeda acknowledges Tyr's authority. They locate the Genite base, guarded by Seraphim carriers, and initiate an attack. The Genites, outmatching the Andromeda, return fire. They demand that the Andromeda surrender, but Tyr keeps fighting, until Andromeda tells him that they have what they came for, and they retreat.

Rommie has analyzed the data that they have taken from the Genite computer. She says that it is not exactly what the Templars said it was, and she thinks the Templars had tampered with the original data they gave.

Beka contacts Dylan and tells him that the Genites are preventing her from landing, but she will try again when things settle down. The Patriarch tells Dylan that he has a drop-ship on the far side of the asteroid. Dylan and Rommie accuse the Patriarch of taking the data from the Genite computers. The Patriarch admits that the virus does not target all genetically-modified humans – only Nietzscheans. He intends to use it as a "deterrant", but Dylan points out that if he wants it to be effective, he has to be willing to use it. Dylan says that Admiral Stark would never have committed or even condoned genocide. The Patriarch responds that 300 years of watching the Nietzscheans in action changed Stark's mind – he is not a descendant of Stark, he *is* Stark. Dylan is, naturally, skeptical, but Rommie verifies that he is not lying. The Patriarch elaborates – Stark's memories and consciousness have been transferred to new volunteer host bodies four times in the past 300 years.

Dylan insists that he is going to make sure that the Patriarch leaves the Genite base, without the bio-weapon. The Patriarch says that Dylan has no choice – he knows that the Maru never left the asteriod, because he has a tracking device planted on it, and there are explosives in the device. He also knows Dylan is reluctant to make sacrifices. Dylan allows him to leave.

A Templar lieutenant questions the Patriarch's wisdom in leaving Dylan alive. The Patriarch backhands the lieutenant, knocking him down. He insists that Dylan is an asset, and he is too valuable to destroy.

Dylan and Rommie return the Maru and leave the asteroid. Rommie locates the Patriarch's device, and determines that she cannot remove it easily, but will be able to back on the Andromeda. She believes, however, that the Patriarch does not want to kill them. Dylan insists that Stark was a good person, and the Patriarch's actions are inconsistent with his claim to be Stark. Rommie observes that 300 years, watching civilization fall, and blaming yourself, could inspire a deep hatred of Nietzscheans. Dylan concludes that even if the Patriarch does have Stark's memories, he is not Stark.

A message arrives from Dylan's Commonwealth contact. She says that she is unsure what advice to give to Dylan, but he should do what he has to do, and she will back him.

Harper expresses his faith in Dylan to find some way to defeat the Patriarch, but Dylan says that he is going to give up, calling it a "strategic withdrawal". He says he will be ready for the next time. Beka is astounded – she says that she cannot believe it is really Dylan saying those things. She expects Dylan, who was willing to call down fire on his own position, to be more tenacious. Dylan counters that the Genites and Templars have left, and he cannot fight those he cannot find. Beka wonders if Dylan thinks he cannot beat the Patriarch, because if he is really Stark, he knows Dylan too well, but she is sure that he can.

Suddenly, Dylan has a change of heart – he thinks he knows where to look. First, he sends the Andromeda (with Beka in command) back to Heimdahl, where he engages some Genite ships in combat, then retreats to Slipstream. Meanwhile, he and Rommie return to the Genite asteroid installation, where they find the Templars doubling back. The Andromeda arrives, and starts firing on the Templars.

Dylan finds the Patriarch back on the asteroid. The Patriarch observes that the Andromeda is outnumbered, but Dylan informs him that the Genites are on the way, and will kill whoever is left. He says that he will destroy the asteroid base rather than let it fall into Templar hands. He admits to being reluctant to make sacrifices, but says that the Patriarch was underestimating him in thinking he would never make them. He suggests to the Patriarch that they cooperate against the Genites, but destroy the base (and the information about the bio-weapon).

The Patriarch gives in, and orders the Templars to engage the Genites instead of the Andromeda. He also sets the self-destruct sequence for the base, but he warns Dylan that the Nietzscheans are a real threat, and must be dealt with.

Dylan is not going to let the Patriarch leave, but the Patriarch insists that he is well-connected, and if he is arrested, he will be set free. If Dylan kills him, he compromises his ideals, and "loses his soul."

Dylan realizes that this is what happened to Stark – she made too many compromises. He lets the Patriarch escape.

Afterwards, Dylan and Beka talk. Dylan wonders if he was right to let the Patriarch go, and wonders why the Patriarch let him go. He observes that this encounter ended in a draw, but vows to find a way to win the next time they meet.