Synopsis of 03×11: A mysterious facility holds the answers to past mysteries and a preview into future conflicts.
Three is back to having weird dreams again. This time he’s got a bad feeling about Nova17. Two and Six debate whether it’s safe to investigate Nova17. Three tells Two and Six that he has a bad feeling about Nova17. Two asks if it has anything to do with Sarah and he says no.
Android calls the entire crew to the bridge, fishing for compliments about her new look. After boosting sensors Android discovers a network of unmanned security sensors surrounding Nova17. The team uses the backdoor override that Dr. Shaw gave to Two to disable the satellites. Three is surprised when the command works.
Two orders the crew to suit up so they can investigate the facility. Meanwhile, Android visits Three because she detects fear in him, and asks if he’s okay because she is worried about him. Three claims that the information on Nova17 doesn’t seem reliable. He doesn’t think that what Victor did is believable, but Android believes it is reliable and questions him not trusting Victor once again.
Two and Android have a discussion about her new look, including the exposed boobs. Android acknowledges after meeting Dr. Shaw, she realizes how special she is and that she has the autonomy to control her own fate. Two and Android hug and Android also thanks Two for being a friend. Oh yeah and Android enjoys saying the word boobs, ha!
Android detects an anomaly on the facility; Three, Six, and Two arrive and find the facility empty. They keep searching and discover stasis pods filled with human-like bodies. Two investigates and finds they are biosynthetic organisms just like her. Six continues to look around and finds there are hundreds of stasis pods filled with biosynthetic organisms in a storage unit. Two realizes this might be the Dwarf Star Conspiracy that future Five warned Android about. Five discovers each organism has been assigned identity.
Before the crew can investigate further, a Mikkei destroyer arrives. Two decides to cooperate with the Mikkei. When the Mikkei arrives on the Dwarf Star facility they ask the crew to turn in their weapons; but the crew resists. A Mikkei doctor confirms that the stasis pods contain assimilated humans. Two claims the Mikkei now have enough evidence to draw a GA case against Dwarf Star and to arrest Alexander Rook. But the commander can’t charge Dwarf Star because Rook has been missing for over two months. The Mikkei commander plans to keep a few of the simulants and to destroy the others. Six believes he should consider letting them live, but the commander disagrees.
Together, the Mikkei soldiers and the Raza crew investigate an anomaly on the facility that appears to look like a red wall. The same red wall that Three dreamed about. Three tells Two and Six that he’s been there before and then he suddenly starts seizing. Two and Six ask the commander if they can take him back to the ship, but he tells them no, nobody is leaving the facility until he figures out what’s going on.
The team finds a sickbay on the facility and waits for Three to come to. When he does, Two asks him what he meant by him being there before. Three confesses that he dreamed about the anomaly. When the lieutenant walks in, Three freaks out and begins to hear voices in his head. He tells the crew they need to leave the facility, that “they” are coming. Two and Six are trying to calm him down when the doctor sedates him. Two asks the commander if she and her crew can leave, and he turns her down again.
The commander decides to wake one of the simulants and torture it to figure out what is going on. Meanwhile, Three escapes from the sickbay and the commander sends his soldiers to find him. Two and Six head off to find Three first before the Mikkei soldiers open fire on him. The Mikkei lieutenant locks up the simulant and returns to shoot the commander in the head. Turns out she has the black alien life form that Three had in him from season 2, episode 9.
The lieutenant takes command and directs all the Mikkei soldiers to shoot the Raza crew on sight, as they’ve killed the commander. Thankfully, Two and Six find Three unconscious near the anomaly before the soldiers do. Back on the Raza, Five reveals to the crew that there was a batch of simulants that woke months ago and that the lieutenant is one of them.
While Three is unconscious, he talks to the alien life form who appear to him as Raza crew members. He discovers that they gave Alexander Rook the technology to create the simulants so that they could inhabit the organisms and invade the galaxy. The doctor and Mikkei soldiers stumble upon Two, Three, and Six. Two convinces the doctor that the lieutenant is a simulant and he takes over command. He directs the soldiers to seize her, but it’s too late as the alien life forms are released.
Two sends Three and Six back to the Marauder while she and the doctor head for the Mikkei Destroyer. But the aliens cut them off and the doctor calls in a nuclear strike to destroy the entire facility, then shoots himself in the head. Three and Six make it back to the Raza only to find that Two never made it to the Mikkei ship and that there’s a nuclear bomb headed straight toward the facility. Five tries to destroy the bomb but the Mikkei ship intercepts it. The Raza crew watches the facility get destroyed and assumes that Two is dead.
Only she isn’t, Android detected a ship leaving the planet right before the explosion. It’s the alt-Boone who saves Two’s life. Two wakes up on the alt-Marauder, tied up and asking what the hell is going on. Boone just smiles back at her. Where could he possibly be taking her? And what will the real Raza crew do to get her back?