Caroline seems to have no choice but to become an “Active” in the “Dollhouse.” A mysterious and secret organisation who reprogram their “Actives” with a new personality for each mission they are hired for. They claim to be doing good. Caroline becomes Echo and one day she is partying with a guy, the next she is a hostage negotiator, in between she is a blank slate living a child like existence. As the negotiator she tries to deal with a gang who have kidnapped a rich man’s daughter. To become a skilled negotiator she is given the memories of a real woman who was abused when she was kidnapped as a child. Now Echo comes across this woman’s kidnapper and ruins the trade off. Echo’s handler Boyd argues with their boss Adelle to allow Echo to continue with the mission. She relents and Echo frees the girl with a little help from another “Active” Sierra. Working at the Dollhouse are arrogant tech guy Topher and seemingly kind doctor Claire Saunders. Outside the Dollhouse FBI agent Paul Ballard is under instructions from high up to uncover its secrets. Someone who knows who Caroline is is also killing and encouraging Ballard’s investigation.

Echo is hired by rich thrill-seeker Richard Connell who takes her out hunting before she realises that she is his true prey. Boyd is attacked in his surveillance van but subdues the attacker. He tries to help Echo but Connell shoots him with an arrow. Echo eventually Connell though she is haunted along the way by memories both of when she was Caroline and of being in the Dollhouse. It turns out that escaped Active Alpha hired Connell to test Echo in some way. He also sends a photo of her to Agent Ballard who continues his lonely search for the Dollhouse. We also flashback to when Boyd joined the Dollhouse with Alpha having slaughtered his predecessor, several other Actives and cut up Dr Saunders’ face.

Echo becomes pop diva Rayna Russel’s new backup singer. Russel is being stalked and her life is under threat, Echo is programmed to unconsciously want to protect her. Sierra is sent along as backup in the persona of Rayna’s number one fan. When Echo thwarts an attempted assassination, the crazed fan takes Sierra hostage and forces a confrontation with Echo and Rayna. Echo’s successful but unorthodox methods provoke a variety of reactions from the staff of the Dollhouse. Meanwhile active Victor in the guise of criminal Lubov sets up Agent Ballard to be killed.

Echo is stealing one of the Elgin marbles from a hotel when her mind is remotely wiped and she returns to her innocent state. As her co-conspirators try to escape from the vault they are trapped in Sierra is loaded with the same personality to talk Echo through her next move. Echo escapes in the shootout with the guards but Topher realises Alpha was responsible for the wipe. Agent Ballard refuses to help Lubov (Victor) who the Borodins now want to kill and throws him back out onto the street.

Echo is made blind so that she can infiltrate a religious cult in Arizona. Boyd works with the ATF agents who are watching the cult leader Jonas Sparrow. They see a cache of guns stored in the compound and prepare to storm in. But they trip the alarm and Echo’s sight returns. Jonas decides to burn down the compound and Echo helps his followers escape. Meanwhile Ballard receives the video of Echo from Alpha and then sees her on the news. And at the Dollhouse, Topher and Dr Saunders realise that Victor is attracted to Sierra which he shouldn’t be while in his doll state.

A journalist prepares a piece about the urban legend which is the Dollhouse and exposes the differing views which the public has about it. Agent Ballard follows some money transfers and tracks down internet mogul Joel Mynor on an engagement with Echo. Mynor tells Ballard that he won’t be able to arrest him and suggests that what he’s doing is just a harmless fantasy. Ballard sleeps with Mellie and confesses the case details to her. Echo is sent out to frame Ballard and get him pulled off the case. But someone within the Dollhouse edits her personality to send Ballard a message about how to discover the truth. Meanwhile Sierra’s handler Hearn has been raping her and is exposed by Boyd. Adelle sends Hearn to kill Mellie but then activates Mellie (who is an active) so that she can dispatch him.

We flashback to see idealist Caroline and her boyfriend Leo breaking into the Rossum Corporation’s research facility on Fremont College Campus. They discover experiments being done on foetuses as well as animals. Security kills Leo and Caroline is captured and is offered a deal by Adelle. In the present a student dies in the Rossum lab from being exposed to a new memory drug. A team of actives led by Victor arrive to sedate the infected students. But the infection spreads by touch and soon Laurence and Boyd are affected too. Eventually the dolls start glitching and remembering traumatic events. Back at the Dollhouse Topher injects November (Mellie) who then passes it to him and Adelle. Echo is on another engagement but when she sees Rossum on the news she rushes over there and helps Sam break into the lab. Once there Sam tries to steal the drug to sell it but is caught by Boyd and offered a deal by Adelle.

Adelle gathers her senior staff to discuss how to stop the actives from glitching. Dr Saunders suggests they allow the affected actives to resolve the issues which are causing them to glitch. Echo, Sierra, Victor, November and Mike all wake up in their pods with their original personalities but no memories. They try to fit in with the other actives but Mike is found out and wiped. The other four escape but Echo returns to try and free the other actives. November remembers her dead daughter Katie and goes to her grave. Sierra and Victor confront the man who brought her to the Dollhouse. Echo takes a gun and forces Adelle to free all the other actives. Once each of them reaches emotional closure they fall asleep. Meanwhile Ballard wakes from a dream wondering how the Dollhouse knew that he had talked to Mellie about them. So he searches his apartment and finds a bug. Then he gets a phone message from Caroline who found his name in her file.

Topher finds a chip which he fears has been used to change his imprints. Laurence is temporarily in charge and locks down the Dollhouse. When they discover that the chip is owned by the NSA he sends Sierra to their headquarters to find out who the spy is. November returns to spy on Paul but she has been reprogrammed to warn him of who she truly is. Victor heads out for his tenth engagement with Miss Lonely Hearts, an older woman. But once there he leaves her and secretly meets with Adelle. Echo volunteers to be imprinted by Topher and help solve the mystery. She is now a spy hunter and interviews the staff of the Dollhouse. Ivy is in the NSA records but Echo works out that Laurence planted that information and is actually working with the NSA. Adelle orders him to have him sent to the Attic. He shoots her just before being wiped but she shrugs it off. Topher tells her of Echo’s learning curve but Adelle seems happy with her evolution.

Wealthy horse lover Margaret Bashford wakes up in Echo’s body and Adelle has to tell her that she died. She had suspected she might be murdered and had “backed up” her own personality in case. She heads to her own funeral and begins to see how her family really felt about her. It turns out her son Nicolas killed her to pay off his gambling debts. She is able to rewrite her will and tell her family how she really feels about them. Meanwhile for Topher’s birthday he is allowed to programme Sierra to be his gaming buddy for the day. Paul Ballard runs Mellie’s prints through the FBI databases and sees the records get deleted. His own dark feelings about her and who she is begin to come out.

Echo is helping a girl who is struggling with memories of abuse. Adelle gets Laurence Dominic’s personality out of the attic and into Victor to help open a message from Alpha. Alpha has killed someone in Tucson and Sierra is dispatched as a forensic specialist to check it out. Paul Ballard breaks up with Mellie. He follows her as she is picked up by her handler and taken to the Dollhouse. He investigates the Dollhouse building and tracks down the man who must have helped design their underground building. Stephen Kepler is growing his own marijuana and is extremely tense about breaking into the Dollhouse. But they do and Ballard and Langdon fight over the confused Echo. Kepler keeps the other actives sleeping and the alarms quiet until he reveals that he is Alpha. He slashes Victor’s face and intimidates Dr Saunders. Then he takes Echo to the chair, she wakes and makes out with him before they leave together.

In flashback we see a self aware Alpha develop feelings for new doll Echo. He is jealous that Whisky is the most requested active and so cuts up her face. He struggles as his handler prepares to wipe him and accidentally has all his imprints forced into his brain. He then goes on a killing spree including the former male Dr Saunders.

In Los Angeles in 2019 a small band of people with their own minds still in tact stumble upon the Dollhouse. Being so far underground they think they will be safe from the technology which can now remotely wipe their minds. They find the chair and use it to gather memories from its former inhabitants to discover how the world changed ten years before.