Epitaph One takes place about ten years in the future. The world is a mess with the Dollhouse's remote wiping and imprinting technology being used as weapons. Reference is made to China having previously laid down a blanket signal on the United States. The Dollhouse technology has been developed to be able to be transmitted through nearly any technology: tv, radio, telephones, etc. With one robocall, a foreign government can turn everyone who answers the phone into a mindless killing machine who works with one goal: kill everyone not imprinted to kill everyone. An instant, huge army that doesn't have to be transported into another country in order to attack.
Few people remain who aren't imprinted, and some who are still their original selves are trying to escape. They travel underground to hopefully avoid the reach of imprinting signals, and in so doing come across the L.A. Dollhouse. The place is empty and dark, but they find the imprinting chair and a list of memories preprogrammed in a sort of playlist. They load the memories up in one guy who've they brought with them that is a "dumbshow", aka he's essentially in a blank doll-like state.
The memories show the progression of how things went down.
We get the scene of Boyd and Saunders lamenting that they don't have enough time together because Boyd's going on the run.
We see Adelle confronted by another head of a Dollhouse who has his personality imprinted in Victor. He informs her that the Dollhouse now provides "full anatomy upgrades" for a high monetary fee. Adelle protests that active's bodies belong to another's soul, and he responds that it doesn't matter, soon it will all be made perfectly legal (a foreshadowing of the Dollhouse having a Doll for a senator seen in season two). He tells her that she can take Victor's body back from him, but that he is currently imprinted in dolls in many other Dollhouses having the same conversation with other Dollhouse heads and that if Adelle removes him from Victor, they'll know what side she's picked: with them or against them.
We see Adelle have a conversation with Laurence Dominic, whom she's removed from the Attic because everything's gone to hell and she needs his help. She informs him that there is a cure that would help block the imprinting process and that that cure is found in Caroline.
We see Tony (Victor) and Priya (Sierra) have a conversation. The LA Dollhouse has cut itself off from the rest of the world and locked themselves inside hoping to wait out the hell that's playing out on the surface of the planet. Something's happened between Tony and Priya (we don't know what), but they're not as close as they once were. Tony beseaches Priya to take her medication, but she says that if not taking it is the price of remaining herself, she's willing to pay it. Priya comments about how sometimes she feels like going to the surface and taking her chance, but Tony warns about how she could end up like November. My guess about some of the not fully explained in this scene is that the medicine Priya declines to take is whatever is made out of Caroline's spinal fluid and that the way it works is that in order to prevent them from being able to be overcome by an imprinting process is to tear down the barriers between all their past imprints blurring them into one multi-mind like Echo, and that Priya's refusal of the medicine is because she wants to remain Priya alone and not become Sierra with all her past imprints. That's my guess, but it's not exactly spelled out.
We see Whiskey, with her scars now repaired, back under the Doc Saunders personality tell Adelle that Topher won't take his medication. Adelle goes to visit Topher, who's living in one of the Doll's pods with tons of his stuff piled all around. He's muttering to himself writing on the wall. He's nearly lost his mind and barely coherent. Adelle tries to comfort him. And in one of the most painfully emotional scenes in the entire show, Topher tells her he's figured out how wipe and imprint people through the telephone. He realizes that that's how things went so bad. He begs Adelle to not answer the phone (there's no actual phone call, he's speaking anticipatorially). He then comments that such a development in the imprinting technology is genius and questions why he didn't think of it before. And then it dawns on him: he did. He realizes that he created the tech that destroyed the world. He starts to lament about whether when he tries to figure something out if it is an act of curiosity or arrogance. He starts crying, "I know what I know" over and over again, and Adelle holds him close until a bang comes from outside.
She rushes out to find Tony and several of the others holding guns at the ready -- Adelle takes one too -- and they're trained on a cinderblock wall that is the sole entrance into the Dollhouse. From the otherside Echo and Paul Ballard break through. Echo is there to rescue them and take them to a location that is safe from imprinting, which is something that Echo credits Alpha for having established. Echo wants Topher to make a backup of her personality since she knows where they're going, but Whiskey tells her she'll have to do it because Topher never goes up to his office anymore. Echo plans on leaving a copy of herself behind in case anyone makes it to the Dollhouse can use it to follow where they're going. Echo and Adelle have a bit of a conversation about whether Echo is only going to save the dolls or if she's going to save everyone; Echo cocks a gun, but that scene ends.
Back in the future, the few people who've stumbled upon the Dollhouse eventually encounter Whiskey, who's only in a Doll state, though she knows enough to help them with imprinting the memories and the back up Echo to know where to go to try to get to safety. The put the backup of Echo in a young girl's body, who turned out wasn't the young girl anymore but someone else who had been displaced into the young girl's body and was intent on killing them in effort to try to get out of the little girl's body. Once Echo is in the little girl, she recognizes jubilantly Doc Saunders, until she finds out that Whiskey is just Whiskey now.
"Butchers" -- people who've been imprinted to kill those who aren't imprinted to kill -- break into the Dollhouse. The remaining survivors flee, but despite them trying to get Whiskey to come with them, she refuses stating over and over again that she "has to stay" (or maybe it's that she "has to wait", I can't remember exactly which phrase). As they survivors flee, Whiskey activates some gas system in the Dollhouse either putting the Butchers and herself to sleep or killing them, which exactly isn't revealed.
The survivors, led by Echo climb up the elevator shaft to Adelle's former office. There, they see out the window to all the other skyscrapers now broken and shattered. On the wall of the office is a bunch of pictures taped to the wall under the banner "Always Remember". There are pictures of Victor, Sierra, November, and Echo in amongst the pictures. Echo takes the picture of herself off the wall momentarily and comments that she hopes she finds herself alive when they get where they're going. They depart the office by climbing up a rope ladder out the window that must've been left there from when Echo led the dolls out of the Dollhouse.
And that's where Epitaph One ends.