Beka is investigating the mining planet of Birrin and unable to communicate with the Andromeda due to the rich ore content in the soil. Dylan is worried about not being able to raise Beka while she checks out reports of hostile activity. He and Trance take a Slipfighter down and find Beka under attack, nearly overwhelmed by Maggog. After mopping up the ambushers, they determine the enemy is on its way to scour the planet for resources. Suddenly a giant Maggog satellite ship moves into orbit, blocking out the sun.

Rommie, the Andromeda’s humanoid avatar, sees the satellite ship moving into position with a host of Swarm fighters. Sensing the satellite ship’s vulnerability, she orders Harper to pilot the Andromeda to Slipstream. He successfully navigates through it but they are immediately beset by Swarm fighters upon exiting. Rommie orders missiles deployed but the system doesn’t respond. Rhade and Harper manage to fight off the fighters with manual controls, but the last one escapes to Slipstream as the fire controls cease to function. The Andromeda AI ignores Rommie's orders for their coordinates, so Rhade leaves in a Slipfighter to lead Dylan, Beka and Trance back in the Eureka Maru.

Rommie’s attempt and failure to access the most mundane functions causes her hologram to appear, informing her that a malfunction in her processor targets her as a threat to the ship and crew. Her reaction to the Maggog was to flee, thereby stranding Dylan and failing her chief function, never to leave her captain. AI is now running an irreversible safety sequence to correct the error, leaving the ship adrift with all functions inaccessible.

Rhade in his Slipfighter finds the Eureka Maru hiding from the Maggog. The two ships race past the enemy fighters, heading straight for a giant asteroid. The pursing ships fire but miss, pulverizing the asteroid into a giant cloud that masks Rhade docking with the Eureka and their escape to Slipstream. They reach the Andromeda and must open the hanger doors manually since all onboard systems are shut down.

Once inside, Dylan is furious. When he questions the hologram, it informs him that his own feelings towards the ship’s avatar have been considered in the program that’s now running to rid the system of any malfunctions. The program is operating independently with impunity; nothing will shut it off short of erasing Rommie’s personality, starting her back at square one. Dylan refuses to do that and storms off to chastise Harper, who devised the program. He later finds Beka on command, attempting to elicit any response from the computers. Dylan pleads with Andromeda, informing her that the Maggog could attack at any moment. The ship refuses, saying it will only respond to the most immediate threat — which has suddenly changed as Harper tries to hack into the security systems and override the program. Andromeda responds by shutting down power throughout the ship. Rommie finds Harper and sends him to meet Dylan and the others, then leaves to defy orders and erase her memory, the only way to ensure the crew's safety.

The ship is rapidly cooling so everyone retreats to the Eureka where they can detect the approach of any Maggog. Any attempt to fight the satellite ship with the Eureka would be fruitless, so they decide to use the bucky cables to turn the Andromeda toward the most likely Slipstream point, in order to manually fire the negative-energy bomb. Dylan and Harper put on heat patches to fight the cold and go with Trance to Andromeda's missile silo to prep the weapon.

With the manual aim ready, Rhade and Beka take off in the Eureka and snag the Andromeda, maneuvering the huge ship into position. They ready it just in time, as alarms begin to sound in the Eureka cockpit: The planetary satellite ship has just exited Slipstream and is sizing up the Andromeda. As it closes in, Harper is frantically punching its coordinates into the firing computer when he notices the Andromeda's systems rebooting. It can only mean one thing — and he informs Dylan but they haven’t time to mourn.

Dylan uses the opportunity to jumpstart the weapon’s trigger, accessing it through a crawl space. Harper warns that the satellite ship has warmed its point-singularity device and is preparing to fire — just as the Andromeda shudders with the launch of its own devastating weapon. The powerful missile arcs toward its target and connects, shattering the Maggog ship in a brilliant light. The Andromeda's systems come back online just as swarm ships move in with a vengeance. Rhade activates the missile tubes and easily dispatches the enemy, leaving everyone a chance to let it sink in that Rommie as they knew her is gone.

Harper and Dylan search the corridors and find Rommie with her usual physical characteristics but with none of the humanity they knew in her face. She scans them and greets them per her programming, but offers no recognition other than that. Dylan orders the erase reversed and Harper reaches for Rommie’s neck to power her down — but she flings him against the wall. She advances on him but then hesitatess as though recalling memories of herself and Harper. She takes another step but stops again when Dylan speaks to her. Rommie is confused and not quite connecting with her past. Harper is convinced that at some point in an AI's life, the sum of its experience actually defines them, outweighing the core programming. She attempts to finish the erasure but Dylan turns her off as her back is turned. They hardwire Rommie into the console and restore her memory.

Rommie wakes with full recognition, and Dylan summons the ship's hologram and AI. He addresses all three, confirming full permissions have been restored and impressing upon them how the uniqueness of each completes the others. Upon making sure this fail-safe will never occur again, he orders the ship to Slipstream.