A few months have passed, and some of the cracks in the Dollhouse's facade are becoming more visible. Paul has become a "client" of the Dollhouse. He has Echo helping to infiltrate a wealthy, charismatic merchant in "things", a man even the FBI couldn't touch, by becoming his bride. Echo, though, sporadically flashes past imprints, presumably due to Alpha's tampering. Whiskey/Dr. Saunders struggles with her newly conscious awareness of her status as an active and makes Topher the target of her confused responses. Meanwhile, Boyd personally interacts with Saunders in a risky fashion.

Topher takes imprinting to the next step by making glandular changes to Echo to allow her to become the mother of a newborn child. However, the alterations soon have an unexpected side effect. Meanwhile, Adelle visits November and urges her to come in for a check-up, and Senator Perrin gains new information on the Rossum Corporation's activities from an unknown source.

When an important client of the Dollhouse, who is also a significant shareholder in the Rossum Corporation, asks for help with a relative who has been struck by a car and lies in a coma, Adelle volunteers the services of the Dollhouse's technical people to attempt to revive him. However, they soon realize the client's relative is a serial killer, and has several intended victims imprisoned. An active is imprinted with the relative's personality but things go wrong. Meanwhile, Caroline is assigned to become a ditzy female student for a Medaeval Literature professor with a fantasy of being seduced by one of his students.

How Sierra came to the Dollhouse is revealed as all the sordid details come to the attentions of Adelle, Topher, and Boyd. The moral dilemmas give each of them great pause as they struggle to deal with the wrongs done to her. Boyd also becomes aware that Echo is not as clearly wiped as she is supposed to be.

November turns up as a guest of honor at Senator Perrin's press conference, denouncing what the L.A. Dollhouse 'did' to her. Echo is sent to collect incriminating evidence against Perrin, and Adelle and Topher travel to Washington, D.C., where they interact with the DC Dollhouse's director, and its genius programmer, Bennett Halverson, who has a less-than perfect past connection to Echo/Caroline.

Bennett's nature and motivation is partly revealed when Echo winds up in her hands, including part of her history with Echo/Caroline. At the same time, Adelle faces off against the powerful head of the DC Dollhouse. Meanwhile, Victor is imprinted with Topher's persona, to assist in Topher's personal espionage, under Adelle's direction, against the DC Dollhouse's plans.

Echo, still in a Doll state, flees, and innocently gets a young Spanish girl arrested. Three months later, Harding has taken over control of the House, reducing Adele to performing menial tasks as his assistant, while putting Topher onto R&D. In the course of performing the R&D, Topher has a flash of genius and realizes the dangerous technology Rossum is actually out to create.

Alpha resurfaces, and the Dollhouse becomes aware of it as the body count of Echo's former clients rises. Alpha's deeper plan goes into effect, with disastrous consequences for one of the Dollhouse's staff as the Actives turn against their handlers.

When his contract with the Dollhouse expires, Victor is released back into the world. There are forces at work in Rossum, however, which have other uses for a man with his extensive military background. Meanwhile, Adelle deals with her underlying personal issues which Victor had formerly provided an out for.

Adelle decides Echo is too dangerous, and arranges for her to be sent to the Attic. Once there, Echo must uncover the Attic's secrets in order to survive.

With the full knowledge of Rossum's strengths and weaknesses, and armed with the knowledge of the result if they don't stop it, Echo, Adelle, and the others begin to put into effect their plan to stop Rossum. Echo must imprint herself with Caroline, in order to get the final piece of information which she alone has, and must confront Bennett, while Paul must adjust to his status as a Doll. Whiskey (Dr. Claire Saunders) finally returns to the Dollhouse as things come to a head, but one final twist has yet to be revealed.

Echo and the crew head to Arizona for the final showdown with Rossum, with Echo drugged and disabled, and everyone unaware of the mole in their presence. Meanwhile, the mole's purpose in encouraging the development of Echo is revealed.

It's 2020, and Topher's virus has eliminated the problem of broadcast imprinting, but the remnants of the blanking and imprinting still remain, creating the world seen in Epitaph One.

Topher has a fix, though... but it requires a return to the place where it all began, and may well cost some lives in the process.