Five dreams of when Three originally found her on the ship as a stowaway. Two and Three wanted to sell her; One and Six wanted to keep her; Four gave the tie-breaking vote and she was made an official (-ish) crew member of the Raza. She remembers hiding a small yet important-looking chip under a table, then wakes up.
The Android tells Two that the explosion at the Mikkei Corporation lab that caused the entire damn planet to blow up was likely the result of a white hole. Research into white hole technology is illegal because it would throw off the balance of power among the corporations. Everyone at the research facility (15,000 people!) was vaporized in the blast.
The gang gets a call from Tabor Calchek, their agent, who claims the Mikkei Corporation thinks the Raza set them up. Two calls BS on that, and says that both Mikkei and the Raza were pawns in the Traugott Corporation's game. Calchek says now that they've proven themselves to be the best -- and burned every other bridge -- the Ferrous Corporation wants to work with them again. Ferrous needs them to rescue a kidnapped employee from a lab on a distant planet. To everyone's surprise, Two agrees to do it.
As Five finds the chip that she hid in her dream, Two tells One that she's anxious about the fact that she's an engineered creation -- officially, illegal tech. Are her thoughts and feelings her own, or somebody else's? One tells her that no matter what, he still loves her (oh, One). She rolls her eyes but seems sort of happy.
All but Five head off on their rescue mission. One, Two and Three break into the research lab but soon find themselves surrounded by men with guns. A bearded leader type, Alexander Rook (Wil Wheaton), says "Welcome back, Rebecca," and knocks Two unconscious by pressing a button. On the Marauder, Four and Six get word that they need to "join the group for dinner." If they try to leave, they'll be killed.
Alex owns Dwarf Star Technologies, which apparently creates entities like Two/Rebecca. Over dinner, he thanks the Raza gang for keeping Two safe and returning her. Alex claims she has a "neural flaw" that makes her prone to fits of violence (sounds right, admittedly); she killed a bunch of techs when she escaped, and will likely eventually turn on her Raza companions. He's set up a dampening field in the lab that weakens her to ensure she doesn't escape again.
After Alex's minions tell him that the Raza is gone, he menacingly announces that he'll now "go to work" on Two. She wakes up, furious that Alex sent away her crew. She tries to beat him up but can't due to the dampening field.
Alex explains that Two is a perfect creation and can withstand any injury. However, she must age, otherwise people will know her true identity and the authorities will destroy her. She asks why he created her, and he ominously says that's a discussion for a later time.
One of Dwarf Star’s techs examines Two for neural defects. He hates her because she massacred many of his former co-workers when she escaped. She apologizes, and he questions whether she's capable of empathy, based on what he's seen her do. He looks forward to her death so he can dissect her brain. When he leaves, she once again tries to escape.
Back on the Raza, the gang tries to come up with a plan to rescue Two. If they land the Marauder, they'll be killed, though The Android tells them that she can get into the facility without their landing. Six tells Five that they need to leave her behind; if the gang doesn't return in four hours, the Raza will automatically take her to the nearest space station.
The Android's clone thinks that she's violating her responsibility to the ship by leaving it to help the crew. The Android says that it's in the ship's best interest for her to help save Two ... plus she's her friend. The clone says that humans don't really feel anything for Androids and the fact that she feels for them means that she's faulty. The Android doesn't care.
The Android drops from the Marauder and enters the facility with her "Kill Everyone" hat on. Meanwhile, Alex and his men find Two and tie her to a table. Alex tells her that she failed his test and they're going to have to start over. The angry tech will operate on her -- while she's conscious -- to test her pain receptors.
The dampening field weakens The Android, though she eventually manages to shut it down. This allows Two to turn the power saw back on the tech who was about to open her skull. Massacre time! She kills a few guards and steals a few guns, and eventually she and The Android join forces and blow stuff up ... though Alex seems to have escaped.
Alex visits a mysterious old man in a high-tech bed and tells him not to worry about Two ... and that "a new prototype" is almost ready. The old man says that Two and her Raza pals must die because they know what she is.
Back on the Raza, the gang has an unusually harmonious dinner. Later, Five decodes the audio on the chip that she found ... and is disturbed to hear a recording of Two saying to Three, "We agree, he has to die. Before we go to the mining colony, but after we go into stasis." Conspiracy and intrigue!
Meanwhile, an unknown person takes a shock stick from the weapons cargo. We see The Android greet him or her as a friend before she gets zapped. Who has betrayed her? Who has betrayed us all?!