Claire treats Victor, who uncomprehendingly asks how he can be his best now, and she bitterly tells him he can't -- all he's suited for now is to be an object of pity. She then hacks into Topher's computer and learns for sure she's a Doll, and definitely isn't too happy about it, and also reveals she knows Topher programmed her to hate him.

In the wake of Alpha having revealed himself, Adelle and Boyd discover he not only absconded with Echo, but also gave her an imprint of unknown origin and removed her tracking device. Adelle then turns her attention to Ballard and tells him the story of Alpha and his "technological anomaly," and informs him he took Caroline. They then discover that Alpha has called in a terrorist threat, causing the FBI to show up outside, but Ballard intervenes with Tanaka and tells him about the Dollhouse, which causes him to call off his dogs and leave in disgust -- which is just what he promised Adelle would happen. Her joy is short-lived, though, when she finds out that Alpha took every single imprint ever given to Echo. Ballard agrees to help find Alpha in order to rescue Caroline, and uses his profiling skills to figure out Alpha's game -- when he had his composite event, he destroyed his original personality, and now he's going to do the same to that of Echo. Ballard, of all people, brings up the question of whether their technology can erase a person's soul, and asks who Alpha used to be. Adelle reveals that he was doing hard time for attempted murder, so Boyd and Ballard go to interview a living victim of his, whose face he scarred, and learn from her where he might have taken Echo.

We learn that a few years ago, Alpha and a female Doll disappeared with a client named Lars while sporting imprints not unlike the leads in Natural Born Killers, and Alpha tortured the guy until he gave up the information about them being Dolls -- their personalities were part of his fantasy. While this was going on, the female Doll danced in the shadows, and we're of course supposed to think it was Echo -- but it was actually Whiskey, their "number-one Active." We meet the previous Dr. Saunders, an older male, and then Alpha sees Adelle giving Caroline her welcome tour. Later, we Alpha kiss and confess to the newly-made Echo that he likes her, which earns him a warning from his handler but does nothing to change his feelings. When he hears that Whiskey is the number-one Doll, he brutally slashes up her face while mildly telling her to let Echo have that vaunted status, and then breaks out of his treatment and horrifically put out his handler's eyes before killing Dr. Saunders.

Back in the present, in a car, we see that Alpha and Echo have picked up another passenger -- a blonde woman of random origin who's there against her will, and Alpha takes them both to a room that contains another chair. Echo, who's sporting some kind of trailer-park personality that thinks Alpha is her boyfriend "Bobby," watches as he puts the blonde in it, and while Alpha's hearing voices, they don't stop him from putting Caroline's original personality into the blonde. He explains to Echo that Caroline abandoned her, vacated her life when things got too tough, and she can ascend to something higher, something like he is, by killing her. He then gives Echo an imprint of all her personalities at once to force her own composite event, but when she comes out of it, she attacks Alpha instead of Caroline, because she doesn't see him, or herself, as superior, only empty. Alpha ends up shooting the blonde woman and then threatening to destroy Caroline forever, but Echo's composite personality seems impossible to intimidate, and even though he shoots her in the shoulder, she chases after him as Boyd and Ballard arrive on the scene, the latter of whom fulfills his years-long dream by rescuing the imprint of Caroline's original personality. Alpha, however, escapes, and to find him, Adelle hires Ballard, who gives his service in exchange for Adelle permanently releasing November (real name "Madeleine"), not Echo, from her contract. In the end, Echo, back to her un-composite self, goes to sleep in her pod -- but whispers "Caroline" before she does. Not as good as it could have been, to be honest, but the show certainly deserves to come back. Fingers crossed!