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" that 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.

A client of the Dollhouse comes to Adelle for help with a psychotic family member. Topher accidentally crosses Echo and Victor's imprint's while there both on assignments.

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.

Senator Daniel Perrin is on a mission to expose secrets of the Dollhouse and Echo is sent to put and end to his plan. Adelle and Topher meet programmer Bennett Halverson in Washington DC and discover her mysterious connection to Echo's past.

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.

When Echo's past romantic engagements are found cuddled, the Dollhouse fears that Alpha has returned to seek his revenge. Adelle grows suspicious of Ballard who hopes to find allies in Boyd and Topher. The Actives turn against their handlers, leaving one member of the house permanently mind-wiped.

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.

When Adelle, Boyd, and the rest of the Dollhouse fear that Echo's uncontrollable mind imprints are making her a danger to their goals, they send her to "the Attic" where Echo is forced to face her worst nightmare in order to survive.

With the Rossum conspiracy now fully revealed, Echo and her allies must now make their stand to stop the Rossum Corporation from enslaving the free world. Echo will finally face herself as Caroline, even as Ballard struggles with the facts of his new existence.
Meanwhile, an invasion is incurred upon the Dollhouse, and Whiskey/Dr. Claire Saunders finally returns to the Dollhouse.

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.

In the series finale of Dollhouse, we pick up from the events in "Epitaph 1". Set in the year 2020, Echo and the surviving Dollhouse crew attempt to restore order for a devastating future world before mankind is eliminated forever.