Tyr receives a message, including visual records, of an attack on Nietzscheans by the Knights of Genetic Purity, or "Genites", a group that is attempting to eliminate "impure" humans - i.e those that have been genetically modified. He suggests to Dylan that they should intervene, and Dylan wonders why, with his pride already destroyed, Tyr is taking such an active concern.

Tyr avoids the question, pointing out that this is genocide, and if Dylan wants to have an egalitarian Commonwealth, he is obligated to intervene.

In privacy, Tyr views a message from Freya: The Orca pride are in danger, and she begs for Tyr to prove that he still cares about her, and to come to her aid.

Andromeda can find no obvious pattern to the Genite attacks. Beka says that she wishes Trance were there, because she tends to guess well. Tyr suggests a specific sector, known to be the home of several minor prides. For lack of a better suggestion, they head there.

Beka is worried that Tyr is setting them up for an ambush, but Dylan doesn't believe that Tyr could be working with the Drago-Kazovs, and he feels that, regardless of Tyr's motives, they have to stop the Genites.

Andromeda finds more records of recent attacks. Tyr wants to check on some of the nearby prides, but Dylan insists on gathering more information by examining some of the wreckage. Tyr protests that the rest of the crew's lack of trust of Nietzscheans is impairing their ability to act. Beka still thinks Tyr has an ulterior motive, but Dylan says that he thinks it is personal.

They recover some debris from the Genite ships. It includes a great deal of advanced technology, including weapons, armour, and sensors. Harper says that he does not believe they have a chance against that kind of technology, and suggests that they might be better off to ally with the Genites against the Nietzscheans. Dylan rejects this idea. He points out that the Genites are not just opposed to Nietzscheans, but all genetically modified humans. This makes Harper the only one on the Andromeda that is safe.

Andromeda is hailed by the Genites. They claim to be impressed with Dylan's success against the Nietzscheans. They insist that he should not trust Tyr, because Nietzscheans are inherently treacherous, and Tyr will turn on him. They claim to be doing things "for the benefit of purebred humans". At this, Dylan breaks contact. He is half heavy-gravity worlder, and intends to destroy the Genites.

The Maru leaves the hangar, Beka and Dylan protest that Tyr has taken it without authorization. Amongst the debris from the Genites, a sensor is active. The Andromeda follows the Maru through slipstream. They find the Genites and launch slipfighters. The Genite leader ridicules Dylan for his use of outdated technology, but offers to help him find the Maru and Tyr. They follow the Maru through another slipstream jump, but one slipfighter is left behind.

The Genites hail the Maru. Tyr is not aboard, but Harper is. He says he wants to join them, because he hates Nietzscheans, and admires their technology. He tells them that it was him who left the sensor on, allowing them to overhear Dylan and Beka. The Genites agree to talk to Harper, but when he gets close, he launches missiles at them. Andromeda joins the fight, and Dylan and Beka make a point of telling the Genite leader that they, too, are genetically modified.

Tyr is aboard the slipfighter that was left behind, and goes to the Orca pride and Freya. He offers to take Freya to safety, but she tells him they have a son. Tyr is surprised, but pleased. He asks her why she did not tell him, and she says that she did not know if she could trust him, because he abandoned her. Tyr explains that between Dylan and Guderian, he could not return. Freya tells him that she has protected their son from the rest of the pride, who feel that they were betrayed by his father. She tells Tyr that Dmitri has seized power and taken their son, who is being kept with Olma, the matriarch. She asks Tyr to help the Orca pride evacuate, but Tyr says that he does not care about the Orcas, he only cares about Freya and his son.

Andromeda drives the Genites back. Harper wants to keep fighting, but the Genites launch boarding pods. One attaches to the Maru, and several attach to the Andromeda. The Andromeda destroys the one on the Maru with her Point Defense Lasers, the Maru returns to the hangar, then the Andromeda flies into the outer atmosphere of a nearby planet to brush off the rest.

Tyr goes to retrieve his son, but finds a doll in his place – it is a trap. Dmitri confronts Tyr, saying that he thought Tyr might be here to help the Orcas, but he now sees that he is not. Freya sneaks around behind Dmitri and distracts him, while Tyr grabs him from behind and breaks his neck.

Tyr demands his son, and Olma comes forward, carrying him – Tammerlaine Anasazi. She says that Tyr has proven his worth, and offers to make him Alpha of Orca Pride. Tyr says that he only needs Freya and Tammerlaine, but Olma tells him that Tammerlaine is too important – based on a genetic sample she sent to the best genetic scientists, she believes he is the genetic reincarnation of Drago Musevini. Tyr declares that this was a foolish maneuver, and believes that the rumour of a Nietzschean Messiah is likely what prompted the Genite attacks. He says that he will take Freya and his son and leave.

The Genites have left the Andromeda and gone searching for Tyr. Dylan heads for the Orca pride. Beka and Harper question this, recalling their previous conflict with the Orcas. Dylan tells them that Tyr is likely going to save his wife. Beka and Harper are surprised to hear that Tyr got married. Beka says that if she had known about Tyr's wife, she would have been less suspicious of his motives.

Tyr wants to leave, but Freya tells him that the Orca will not let them leave without a fight. She points out that Tammerlaine is the perfect tool for Tyr's ambitions. Olma tells Tyr that she will give him Tammerlaine when all of the Orca are on the Andromeda, and Tyr must be the last to leave.

Andromeda arrives to find the Genites already in the system where the Orca pride lives, but the Genites are still scanning, indicating that they have still not located the Orcas. Dylan broadcasts a message to Tyr, to both let him know that they are there, and to draw the Genites' attention. He directs Tyr not to reply, but Tyr responds anyway. Rommie says that this was a fatal mistake, but Dylan claims that Tyr does not make mistakes.

Tyr is helping the Orcas evacuate the asteroid, but he holds Freya, Olma, and Tammerlaine back. He does not expect that the Orca have much chance of survival against the Genites.

The Genites land on the Orca asteroid, and take Freya hostage. They demand that the baby be handed over to them. With a look, Freya tells Tyr that their son is more important to her than her own life. Tyr shoots at the Genites that are holding Freya, but they kill her.

The Genites accuse Dylan of protecting the Nietzschean Messiah, who will unite the Nietzscheans, making them even more of a threat. Dylan says that he is only looking out for a member of his crew.

The Orca launch ships, but they are quickly destroyed by the Genites, who then leave.

Dylan searches the system for survivors. Although Andromeda cannot detect any, he insists on continuing the search. Five days later, Tyr returns in the slipfighter, looking shaken. He says that he has lost both his wife and his child. He tells Dylan how the Genites killed Freya, then says that as he and Olma were fleeing, there was an explosion, and Olma was killed. He took his son, but when he got to the slipfighter, he found that Tammerlaine was already dead. He says that he knew Dylan would still come back for him.

Some time later, Dylan asks Tyr about the transmission that gave away his position. He does not believe it was actually a mistake on Tyr's part, and he wonders if Tyr's son is really still alive somewhere, waiting for the time when Tyr can use him for his plans. Tyr says that he only wishes that were true, and Dylan says that he also wishes it were true. Dylan asks if Tyr's son was, in fact, the Nietzschean Messiah. Tyr says that, since he is dead, they will never know.

In his own quarters, Tyr performs a DNA comparison on a lock of hair from his son and one from Drago's remains. The match is perfect.

On a planet somewhere, Olma is caring for Tammerlaine, who is very much alive.