Season 2, Episode 1 - Designate This

Log Line: After being captured and imprisoned at Manticore in last season's finale, Max resists powerful attempts at re-programming and breeding, and plans her escape from the genetics lab. She is aided in her breakout by the gentle but beast-like Joshua, an early Manticore creation from human and animal DNA, who was kept secret from the organization's rank and file. And Logan's obsession with bringing down Manticore has catapulted him to the top of their most wanted list.

OUTLINE:
Eyes Only streams its news about Manticore and its genetically building perfect soldiers. Eyes broadcasts that some of the soldiers are loose on the streets. As Logan longs for the dead Max, the very-much alive Max is really being put through boot camp training at Manticore. Her X-5 designation is 452, but Max is only playing along as a willing soldier.

Madame X shows Max the now-test subject body of Zack. He shot himself so that his heart could be transplanted into the body of Max, saving her. Madame X tells Max that she destroys everyone that she loves, and that Eyes Only will be next -- because she plans to kill him. Later that night, Max slowly chisels through her cell wall, desperate to break free and regain her identity.

With the help of the freedom group S1W, Logan scams his way into the Veterans Administration files to find out where the Manticore facility is. Although he watched her die, Logan can feel that Max is somehow still alive. After lights out, Max is visited by who she thinks is Ben. It isn't really him, but another X-5 that resembles Ben. He is sent to impregnate Max, but she fends him off. She names him Alec. McGinnis contacts Lydecker and asks him to give up Eyes Only in return for his reinstatement.

Max manages to dig through her cell and she climbs into Manticore's basement. There she befriends a transhuman named Joshua, who has traits of a dog and a human. There are others like him being kept secret in underground cells, all fathered by someone named "Sandman." Joshua exhibits powers to rival Max, and he has sonic hearing. He shows her a window and she makes plans to escape. He too wants to be out in the real world. When Max returns to her cell, she is busted by Alec. But he doesn't turn her in.

Lydecker meets with Logan, but it's a setup for him to be captured by McGinnis. Lydecker lets Logan go, and demands from McGinnis to know what's happening to his "kids." McGinnis gives up that Madame X is trying to learn more about the X-5's DNA. Then Lydecker kills him. Madame X is worried that the Committee will be pissed off if Eyes Only broadcasts Manticore's location. She threatens to burn Manticore, with all of the X-series soldiers inside, unless Max helps her find Eyes Only. They get the information out of her. Alec and Joshua help Max escape, and she heads straight for Logan's apartment to save him. He is overjoyed at the sight of her, and kisses her. Suddenly, he crumbles to the ground in pain. Alec is there, and informs them that he injected Max with a genetically targeted retrovirus that goes active with any intimate contact. She has infected Logan with one deadly kiss. But to get the cure, Max has to bring Logan to Manticore and turn herself in.

After kicking Alec's butt, Max helps transmit Logan's last streaming message. She returns to Manticore, finding it engulfed in flames. She manages to unlock the cell doors so that all the X-series and transhumans can escape. Max takes Madame X hostage for the antigen to save Logan. But when a guard shoots at Max, Madame X steps in the bullet's path. She warns Max that she can never be rid of her virus. Before she dies, Madame X tells Max that she is the one they have been looking for. "Find Sandman," X whispers with her last breath.

Logan heals miraculously after being given the antidote, but Max keeps her distance from him to not infect him again. Yet now there are more like her out in the world. She hopes they can keep a low profile like she has done.

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