Beka is on the planet Birrin, with a squad of Lancers. Birrin is surrounded by an asteroid field with high iron and lead content, which interferes with her communications with Andromeda. Dylan and Trance board a slipfighter to check up on her.

Meanwhile, Beka is not having any luck locating the planet's inhabitants. She hears a noise and goes to investigate, but she finds one of her Lancers, infested with Magog eggs. She shoots and kills the eggs, but a group of Magog attack her and the remaining Lancers. A fight ensues, ending when Dylan and Trance arrive. They wonder why the Magog are on Birrin, and speculate that they may be mining the planet's resources. Suddenly, over the horizon comes a ship unlike any they have ever seen before – although it is much smaller than the Worldship, it is twice the size of Andromeda. They dub it a "satellite ship". More Magog attack them.

The satellite ship and a fleet of swarmships move towards the Andromeda. Rommie, worried about Dylan, and remembering the last time she was boarded by Magog, decides to retreat into slipstream. Harper is working on some systems on the Command Deck, but is the only one available to pilot, as no others are answering Rommie's call, so he takes the helm. He protests that he is out of practice as far as piloting goes, so the ride is a little rough.

Rhade is unable to answer Rommie's summons, because he is stuck to the ceiling – the gravity fields in the corridors have, for some reason, been reversed. When Andromeda comes out of slipstream, the fields revert to normal.

Dylan, Trance, and Beka are fighting off the Magog, and find their recent technological advances somewhat disconcerting. They make their way back to the Maru and leave the planet, but find Andromeda gone. Trance quickly analyzes the debris, to ensure that the ship was not destroyed, and the Magog start to attack the Maru.

Andromeda turns to fight a wing of swarmships that followed her through slipstream, but Rommie indicates that she is experiencing problems and is locked out of the ship's systems. Rhade (who tells her, to her surprise, that she ordered the crew to quarters) and Harper take manual control of the weapons and manage to destroy all but one of the swarmships, which leaves, presumably to inform the satellite ship of their location. Rommie says that they need to return and retrieve Dylan and the others.

The Maru ducks behind an asteroid and cuts power, to hide from the Magog.

Rommie finds herself cut off from the main AI, so Rhade takes a slipfighter to find Dylan. Rommie demands an explanation from the AI, and Andromeda tells her that she has detected a fault in Rommie's processor, and she is a threat to the ship. Andromeda further explains that fleeing the Magog and leaving Dylan behind contravenes protocol for a warship, and Rommie's emotions (in this case, fear) are a danger to the ship and crew.

Harper (in his shop) asks Andromeda why he is unable to override this feature, and Andromeda explains that she cancelled his override, because it is not "safe".

Rhade arrives in the Birrin system and contacts the Maru. They devise a plan to lure the Magog into a chase, then use the debris from asteroids as cover to escape. Beka uses the Maru's radar to locate a likely asteroid. The plan works, Rhade lands the slipfighter in the Maru's cargo bay, and they head for the Andromeda.

Andromeda insists that Rommie has a pattern of endangering the crew with her emotional reactions, referring to the incident with Gabriel, which is why she has been cut off from the ship's controls. When the Maru arrives, Andromeda will not open the hangar doors, because her systems are currently shut down, and she insists that she cannot do anything until the analysis is complete. Dylan tells Beka about an emergency door release by the refueling port, and Beka uses the Maru's refueling probe to activate it and gain access to the hangar.

Dylan confronts Andromeda, who tells him that his objectivity cannot be relied on, due to his affection for the avatar. Rommie tells Dylan that her emotions are interfering with her effectiveness, and that she has been isolated from the AI by a program of Harper's, for everyone's safety. She offers a solution: If her avatar's personality is erased, she is no longer a threat. Dylan declines this option, and goes to the slipstream core to find Harper. Beka heads for Command to watch for Magog.

Dylan is angry about the program, but Harper insists it was an emergency safety precaution. Andromeda tells Harper that there is nothing he can do to override it, but Harper is not willing to give up. Dylan warns Andromeda that they are expecting a Magog attack, but Andromeda points out that there are none in the system yet, and she will respond to the greatest current threat – at this point, that is Rommie, but it is changing. Alarms sound, and the ship goes into emergency power-down. The internal defenses start to come online, and the temperature starts to drop.

Rommie tells Harper to get to safety, and she will try to "fix it". Harper tells her not to do anything drastic.

The crew meet in the corridor and attempt to formulate a plan. The crew quarters are safe, but they cannot do anything about the situation from there. They head for the Maru, which, at least, has its own communication and navigation systems.

Rommie accuses Andromeda of turning on the crew. Andromeda insists that Rommie should erase herself, but Rommie points out that Dylan ordered her not to do so. Andromeda insists that it's the right thing to do. Rommie issues the commands to erase her own personality.

Once he has retrieved warm clothing from the Maru, Harper wants to go back and help Rommie, but Dylan stops him. He says that they need to prepare for the imminent Magog attack. To destroy the satellite ship, they will need heavy weapons, such as Andromeda's negative-energy bomb, but they have no access to the ship's systems, so they will have to do it by hand. Dylan and Harper head for the ship's missile silo.

Beka takes the Maru out, and grapples the ship with Bucky cables, in order to turn it to face the slipstream portal. The satellite ship arrives, but does not immediately begin firing. A squad of swarmships soon follows, as Beka is providing targeting information to Dylan and Harper.

Rommie's erasure completes, and Andromeda starts to reboot. Dylan and Harper notice this, and realize what it must mean, but they press on with the job at hand. The missile is still not back online, so Harper suggests hotwiring it. Dylan crawls into the conduit and rewires the system, firing the missile, and destroying the satellite ship.

Dylan and Harper find Rommie in the corridor, but she is acting more "robotic", not like the Rommie they knew. Harper is upset, because this is what his program was meant to prevent: It was supposed to cut the avatar off from the ship's AI, so that this would not be necessary. Harper and Dylan's concern triggers memories deep within Rommie – her memories are not completely gone. They deactivate the avatar so that Harper can restore her personality (and deactivate the "safety" program).

Beka, Rhade, and Trance, on Command, destroy the remaining swarmships.

Rommie apologizes for leaving Dylan behind, but, when prompted, allows that she expected that Dylan would be able to look out for himself, so Dylan says that she did the right thing. Dylan addresses Rommie and the two aspects of the ship's AI (hologram and on-screen): He tells them that he needs all of them, and that they all give something unique.

Rommie is happy to be back.