Echo is one of the "Actives" in the elite and illegal Dollhouse. Through different personality downloads, she plays the role of a lovestruck girl on a romantic weekend, and then a ruthlessly efficient kidnapping negotiator.
Meanwhile, FBI Agent Paul Ballard is struggling with his assignment to uncover information on the Dollhouse. The chase has destroyed his marriage and is wrecking his career, and it doesn't seem that he'll stop until he uncovers the truth.

An outdoorsman hires Dollhouse to program Echo as his perfect counterpart, but their wilderness expedition becomes a survival game. Meanwhile, Ballard tries to learn more about Echo and continues his investigation, and the massacre which led to Boyd's recruitment is revealed.

Echo is turned into a backup singer in order to protect a singing star from her crazed fans. Meanwhile, Agent Ballard continues with his investigation but is set up for an ambush.

Echo's newest programming is for a sassy safecracker, but a sudden interruption during an art theft leaves her without her skills after she's trapped in a vault.. While Adelle calls in Sierra, Topher tries to track down the person responsible. Meanwhile, Ballard deals with Lubov.

Echo is "hired" by a senator to infiltrate a heavily guarded cult and imprinted as a religious believer. However, when she is blinded so that a surveillance camera can be implanted in her eye, her mission is made much more difficult. Meanwhile, Ballard gets one step closer to the Dollhouse with the assistance of his unseen ally, and Topher and Saunders try to pinpoint the sexual connection between Victor and Sierra.

Echo becomes the perfect wife for a lonely internet mogul and Sierra's attacker is revealed. Mellie's life is in danger and Agent Ballard's investigation takes a surprising turn when he comes face-to-face and goes fist-to-fist with Echo for the first time.

The Dollhouse is assigned to a campus by their sponsors, the Rossum Corporation, to deal with the release of a chemical that causes hallucinations and uncontrolled memory recall. Meanwhile, Echo is on another assignment but is drawn to the same campus after she sees a newscast. There she must deal with a few memory recalls of her own.

Echo, Sierra, Victor, and Mellie awaken inside the Dollhouse without either their "Doll" personalities or their own histories. They realize there are others who haven't escaped their programming, and Echo leads an escape attempt. Meanwhile, Ballard finds out more information on the Dollhouse's location, Adelle has a plan to test test the House's security, and the escaping Dolls begin to recover the memories of their original lives.

When a traitor is discovered inside the Dollhouse, Echo and Sierra are programmed as spy hunters to uncover the culprit. Meanwhile, Ballard receives surprising news from Mellie, and Adelle harbors a secret.

Echo is programmed with the memories of a dead woman in the hopes that she can help solve the woman's cuddle. Topher secretly prepares Sierra for an engagement, and Ballard looks into Mellie's past.

Echo uses the story of "Sleeping Beauty" to help a young girl overcome a past trauma, but does the story foreshadow Echo's own future? Meanwhile, Ballard may have found the original designer of the Dollhouse, Adelle goes to the attic for answers, and Alpha reveals himself and his endgame.

Alpha's continued obsession with Echo may cost her everything. Ballard makes a decision that could change the rest of his life. One Doll's story ends as another's is revealed.

The year is 2019, and the world is broken. A small band of survivors discovers an abandoned Dollhouse and as they explore they begin to understand the shadowy organization and to suspect that they may have been responsible for the current state of the world.