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The last time we saw Echo she had been imprinted with all of her previous engagements. Dr. Saunders learns that she was actually a doll, Whiskey. After numerous stunts attempting to reveal the Dollhouse, Agent Ballard is dismissed from the FBI. Enter Season 2.
In this episode, Echo's imprints are all wiped (courtesy of boy genius Topher). She is assigned to new engagement, which has her former handler, Boyd Langton, concerned. The surprise is that the client is actually Paul Ballard. Echo believes she is working with Ballard to take down a criminal he's been pursuing unsuccessfully for years. She's clearly successful in the seduction of the target, Martin Klar, since the episode begins with Echo walking down the aisle.
Dr. Saunders (or Whiskey) seems to be falling apart now that she knows she is a doll. She questions her entire existence. She reaches out to Topher while Langton reaches out to her. Dr. Saunders is jealous of Echo, because Saunders used to be "number one" before Alpha disfigured her. She doesn't know how to move forward since she questions everything - do any of her thoughts and feelings belong to her? Topher explains to her that he is responsible for many of her feelings, but some of them are her own choices and not part of the imprint.
Martin discovers that his new wife is collaborating with his enemy, Paul Ballard. He finds Echo trying to break into a locked drawer in his desk. He attacks her - bashing her head against the desk and asking her WHO ARE YOU? She tries to convince him that she isn't interested in his work and she's only interested in being his wife... she's always be Mrs Eleanor Penn... wait, what's her name again? She slips up and gives the name of one of her previous identities! Klar is pissed and Echo is confused - she's not quite sure who she is at the moment.
It looks like the honeymoon is over before it even started - or is it? Klar whisks Echo off to his private jet and reveals his business plan - he has a major arms deal underway: detonators intended to be combined with plutonium to create dirty bombs.
Ballard has been keeping tabs on Echo all during this mission. He senses something is wrong with Echo and that her handler is not doing the job. Her handler mistook a spike in her readings as sexual excitement, but Topher confirms that it was definitely pain. Ballard doesn't want to jeopardize Echo's safety by sending in the extraction team, so instead he turns himself over to Klar. Ballard tells Klar to let Echo go and tells him that he doesn't know who he's dealing with - Klar doesn't realize that Ballard's talking about Echo herself. Echo is malfunctioning - her various imprints keep slipping out. Ballard antagonizes her, verbally and physically until something he says triggers her ass-kicking goddess and she unleashes on everyone in her path.
Back at the dollhouse, Ballard apologizes to Echo for his behavior, assuming she doesn't really remember anything since she has received a treatment. It seems, however, that Echo remembers nothing and everything at the same time. She says she still feels these other identities - she wants to find these people because they are lost but not gone, as she says. She asks Ballard for his help and we then see them in the treatment room, holding hands and Echo affirming that she trusts him with her life - clearly Ballard has agreed to become Echo's new handler.