A battle with the evil ship, Basilisk, is imminent as Dylan and Beka discuss their plan to defend the fledgling democracy, Mobius. Planning on confrontation in two weeks, Andromeda AI announces the Basilisk task force is assembling much quicker than expected, and will be ready to deploy in forty-eight hours.

On the planet Machen Alpha, Rommie has located her informer, Mister Kim in a seedy hotel room. Rev Bem, Harper and Tyr are onboard the Eureka Maru, ready to aide Rommie in her mission to uncover the plans of the Machenites. Suddenly, planetary security bursts into the hotel room. With blinding speed, Rommie opens fire on the guards. She escapes out the window with Kim under her arm. They land safely, and Kim fearfully realizes Rommie is an android. After Rommie and Kim disappear out the window, a new agent, Carter, enters the fray. He discovers a badly shaken Ngomi, who witnessed the battle. Carter deducts that Rommie must be an AI.

Meanwhile, aboard the Eureka Maru, Harper doubles over in pain from the Magog larvae in his stomach, and has to medicate himself several times. The military detects their satellite network, forcing the Eureka to depart immediately, leaving Rommie and Kim to hide out until Dylan can extract them. Unfortunately, missiles strike the ship while they are cruising over the water, and the Eureka Maru is immersed.

Later on the streets of Machen Alpha, Kim repairs the damage to Rommie's torso. He explains how he helped design the Basilisk to defend his world, not to destroy other planets. He has a moral conflict with helping an A.I. because of what they did after the fall of the Commonwealth, wiping out innocent citizens because they were seen as &quo;nonproductive.&quo;

Dylan decides they must leave the Eureka in the ocean and move on to save Mobius. Meanwhile, onboard the Eureka, Harper races around the engine room trying to repair the damage. As the Magog larvae act up, he continuously medicates himself with his inhaler. Sinking deeper, they lose the ability to communicate with Rommie. Tyr and Rev Bem discover Harper unconscious from overdosing on his medication. When Rommie realizes her friends are in grave danger, Kim is noticeably surprised at the emotion this android is showing.

While the Basilisk is seconds away from Slipstream range and mobilizing to attack Mobius, Ngomi and Carter plan to catch Rommie and her informer. As Rommie and Kim move through the tunnels in search of safety, Kim accuses her of putting him in danger. Rommie reminds him that three of her friends may die because of him. When he realizes that Rommie does indeed have emotions, he hands her a data disk that holds everything she needs to know. In Cyberspace, Rommie steps into a virtual reality version of a large hangar and discovers an intact Magog Swarmship, and decides that she must see this ship for herself.

The Basilisk emerges from Slipstream and engages in battle with Andromeda's combat drones. Dylan realizes they are using point singularity weapons, which means the people of Machen Alpha must be cooperating with the Magog. Beka suggests they put the sensor drones in front of them to alter the PSB’s heading. The offensive missiles are now able to collide with their target, and the Basilisk explodes. Relieved, Dylan heads to Machen Alpha to retrieve the rest of the crew.

On the Eureka, Rev Bem and Tyr decide to fill the ship with water and float to the surface. Rev Bem is able to hold his breath for long periods of time, however there is only one E.V.A. suit for underwater breathing. Tyr believes it will be a waste to let Harper use the suit, as he is already unconscious. Rev Bem convinces Tyr to put Harper in the suit, as Tyr can survive without air for twelve minutes. They hope the cold water will preserve his brain functions until they reach the surface, and he can be revived.

Rommie decides to hijack the Magog Swarmship just as a hologram of Carter with real troops shows up to destroy their plans. As Rommie engages in battle with the troops, Kim opens fire and is shot by the soldiers. Rommie retaliates by killing everyone in the room. Carter jacks into one of the datalinks and finds Rommie before a fusion reactor. She reacts by wreaking havoc on their cyberworld with a toss of her hand. He pleads with her to stop the overload and save millions of people, but she wipes out the cyberworld in its entirety. As the Swarmship hangar is being evacuated because of reactor overload, Rommie dashes in. Carter stands at the door, and Rommie attacks with her force lance while Carter opens fire. As they struggle, Rommie realizes Carter is also an A.I.. He tells her he was one of the original A.I.'s that survived after the Revolution. Rommie throws her lance at his stomach and he catches it, exploding into charred remains. Rommie returns the reactor to normal, alleviating the danger of overload.

Tyr comes to, and realizes they are alive. Harper has been revived as well. Suddenly, a Magog Swarmship approaches Ñ with Rommie at the helm. She clamps down on the Eureka and carries them away to safety. Back onboard Andromeda, Dylan thanks Rommie by placing the Order of the Vedran Empress medal around her neck.