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.
In the year 2019, Los Angeles is devastated. Imprinting technology has gone completely wireless and out of control. People are divided into those who have been "printed" and lost their identities, "Butchers", who will kill just about anybody who isn't killing, and "Actuals", those who are struggling to hold on to their memories and bodies.
A small group of actuals and the father and daughter they are protecting, are on the run, and stumble upon the abandoned Dollhouse. As they find the imprinting chair, they use the father, who had been "printed", to obtain the memories stored within the chair. They learn of the Dollhouse's original purpose, and how Caroline found a way to maintain her original self, even after being imprinted with a new personality. They found out how Clive Ambrose, through Victor's body, tells DeWitt that the Dollhouse will now be offering a new service to their highest paying clients - by selling the bodies of the actives as "upgrades".
The Actuals encounter a half cataonic Saunders/Whiskey, who has been waiting for Boyd to return for her. She leads them to hidden wedges with more memories from former Dollhouse employees and Actives. They found out how most of the former actives, along with DeWitt and Topher, dug-in to the house, prepared to defend themselves from those that would come for their memories and bodies. Caroline and Ballard eventually arrive and announce that, with Alpha's help, they have found a way to defend against unwanted imprinting, and a "Safe Haven." Caroline then has Saunders make a back-up copy of herself, so that the way to "Safe Haven" can be found by others.
After realizing that the little girl has actually been printed with an adult, and she has been the one who attacked some of the Actuals, the survivors Zone and Mag, are able to imprint Caroline's personality on to her. As the butchers find the Dollhouse and come for them, Whiskey turns on a poisonous gas killing them, and possibly herself. Zone, Mag, and the newly imprinted little-girl Caroline, escape into a desolate Los Angeles, hoping to find "Safe Haven", and possibly the real Caroline herself.