Now we come to the discussion of the ending. If you think there have been spoilers before you haven't seen anything yet. If you're going to stop reading, now is the time.
Beck, under threat of an execution order, assists Alan and Alex in kidnapping Dorothy. Beck meets Roger when he arrives at his home and seems slightly apologetic, but Roger dismisses him with an accusation of selling out. In Big-O, Roger almost saves Dorothy but is prevented by a rebuilt Big Duo, piloted by Alan Gabriel. Alan has been connected directly to Big Duo's systems, and wires connect various parts of him (including his eye) to various control ports along the inside of Big Duo's pilot chamber. All during the lead-up to the fight we hear Schwartzwald's voice, as if he were the pilot of Big Duo. (Schwartzwald died off-screen a few episodes earlier.) The fight goes well for Alan, but before he can destroy Roger and Big-O a funny thing happens. While he gloats about his impending victory, the controls seize up, then wires pour out of the various control ports inside Big Duo. The screen inside flashes "YE GUILTY." In a grisly scene the wires fill the pilot chamber and, we guess, smother him. Big Duo then takes off for the sky, and is lost to sight. Beck and Alex look on. Beck suspects Alex knew that would happen. Alex expresses a desire to "reset the city again," but not in the "crude" way his father did it. He offers Beck a place in the new order.
Roger goes searching for Dorothy while Norman, with the help of many of the citizens of Paradigm City, sets about repairing Big-O from the fight with Big Duo. (Looks like your secret's finally out in the open, Roger!) Dorothy's memory circuits have been removed, and her android body is lifeless. According to Norman, there's no way he can repair Dorothy's damaged circuits and things look pretty grim for the sarcastic automaton. Meanwhile, Angel, still torn up over being rejected by Roger in favor of Dorothy and her own indecision when she could have saved Dorothy from Alan a couple of episodes earlier, finds a way down into the tunnels beneath the city. There, she finds a television soundstage that looks exactly like the house in her memories of her childhood! She begins to break down.
Dorothy's lifeless body, resting on a table with no one around, says "Roger."
Roger searches for the people responsible for kidnapping Dorothy, and finds Angel, Vera and Gordon Rosewater, unexpectedly alive, on the stage. Gordon is messily slopping up a bowl of tomato soup. There, it's revealed that almost everyone in Paradigm City is one of Gordon's "tomatoes," the predestined children with the barcodes in their eyes, including his own son Alex and the members of the Union. Vera cannot believe it and seems to kill herself, or maybe she's just making a flashy exit. Gordon remembers that neither Roger nor Angel are among the tomatoes, but that doesn't help Angel, who is soon reduced to a sobbing bundle on the floor. He calls her a "living memory." Roger hears from Norman that the city is getting smashed up, so he goes back upstairs and gets in Big-O.
Upstairs, Alex is in Big Fau, which is now obeying him. On the wall behind his seat is a luminous hourglass-like object, apparently Dorothy's removed memory unit. What Big Fau needed to operate was a "core memory," according to Alex and Beck, to get past the CAST IN THE NAME OF GOD check. Alex begins to run amok in Big Fau, and destroys much of the undomed city, though there seem to be many survivors, including the boy Datsun, who adult Datsun is concerned about. Roger and Big-O confront him as the penultimate episode ends.
The last episode, #26, "The Show Must Go On," begins with a shot of the wreckage of Speakeasy, the bar Roger frequented to get information from Big Ear. While his voice speaks aloud to no one, we see through his smashed-up metal head that he is an android himself. The building collapses on top of him.
The two Bigs fight, while Alex gloats. During the fight, wires spring loose from the sides of Big Fau's pilot chamber and plug themselves into Alex's back! Alex tells the robot, still gloating, that if it's trying to absorb him into its systems that he won't find it so easy, that he's stronger than Seebach or Gabriel. The window in front of Big-O's pilot chamber gets cracked, and Big-O himself tossed into the sea where Roger passes out, the compartment slowly filling with water.
Underground, Angel is still senseless, saying she only ever wanted a memory for herself. Gordon seems sympathetic, but he sees something happen to her (forgot what), and exclaims, "The memory desperately wants to be remembered!" He leads her into an elevator in the side of the TV room and the doors close. As they do, the room disappears, replaced by a blank grid pattern.
Beck has arrived at Roger's house. He seems quiet and thoughtful, quite different from the usual, giddy, feet-clapping Beck. He looks at Dorothy's body fixedly. But then it stands up on its own! Beck freaks out. Dorothy walks outside onto the roof and Beck can't figure out how it's doing it. As near as we can tell, it's because Dorothy has her own memories now, and the ones removed were the ones that belonged to Timothy Weinwright's dead daughter. She stands on the edge of the roof in her customary pose. Norman comes out onto the roof with a wetsuit, with the object of saving Roger, answering Beck's demands to know what's going on by saying that memories "are something that belong to the human form." Beck complains that he hates them both, "the black guy and the white," (meaning Roger and Alex) and points a gun at Norman.
Underwater, Roger is having the strangest flashbacks yet. Among them: Roger the Wanderer (from the first episode of the season), Roger dead in the cockpit of a destroyed Big-O, an assembly line of Roger Smith androids, an action figure of Dorothy, and other weird things concerning young versions of Angel and Vera. In one of the flashbacks, a Big-O poster can be seen in the background. Roger wakes up while wires disconnect from the sides of the chamber and make their way towards Roger's back. Roger tells Big-O, haven't they always fought side-by-side? He asks it if this is what it really wants, to merge with Roger and to become one being. Big-O's interface wires retract. Above ground, Dorothy says aloud that Roger has made his decision.
Under the city, the elevator doors open on floor #666. Angel steps out to a scene that looks a lot like the holodeck from Star Trek. Wings of light sprout from her back, where the scars are, and she flies to a light seen in the distance. Gordon, behind her, holds up his book, Metropolis, and shouts aloud to the unseen director to fill the book with memories. The book's empty second half fills with text, then both he and the book vanish. So does the open elevator door behind him, leaving behind nothing but blank holodeck.
It's Dorothy, in a wet-suit, that comes to Roger's rescue. We get to hear the "You're a louse" line one last time, this time said affectionately?? They get out of the water (they get dragged about by Big Fau a bit), and Dorothy hooks herself into Big-O's circuits. When asked how she knew to do that, she tells Roger it was Beck that told her! This way Big-O is able to progress to it's "final stage," which involves a big-ass laser cannon. Alex starts to get frightened. The cannon fires, cutting a wide swath through the ruins of Paradigm City, destroying the central dome. Big Fau takes heavy damage, with almost an entire side of its body destroyed, but Alex is still alive and is still capable of firing, and Big-O now drained of power is a sitting target.
But... a light appears, and it becomes yet another giant robot, never before seen. Dorothy identifies it as "Big Venus." Wherever it goes, buildings disappear, Big Fau disappears, the whole city disappears, replaced with an impossibly vast blank holodeck-like chamber! That seems to be what Big Duo collided with when it rocketed up into the sky, the roof and ceiling lights of this massive chamber. Soon it's only Big Venus and Big-O, still containing Roger and Dorothy, and Roger remembers what Gordon wanted him to do – negotiate with the director, who he correctly identifies as Angel!
After some dialogue, during which we hear that Roger believes he will not lose his memories of Angel, that he doesn’t know why everyone lost their memories forty years ago, that he himself doesn't know anything about his own past, or where he came from, but is certain that they weren't taken from him, that he likely lost them by his own decision. We see Angel in a control room surrounded by video monitors, crying. Big Venus and Big-O then... merge. And then....
The city is back, just as it was at the start of the show, of the first episode. Roger's car, the Griffon, once again drives down the street. The credits appear on the screen in the same manner and font as they did at the beginning of the first episode. Roger begins one of his old episode-beginning speeches. The camera shows, for a half-second, Angel and a subtly-different Dorothy standing on the side of the road. The Griffon continues on, and Roger says, "My name is Roger Smith. I perform a much-needed service here in the City of Amnesia...." And then....
WE HAVE COME TO TERMS
An' that's the end.