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As mentioned in my review, I spent most of my time watching Nowhere Man speculating on what was actually going on, via a gigantic fanwank. The full episode-by-episode writeup is below. Massive spoilers for the entire series, as well as for Dollhouse.

My theory: In the final episode of the series, it is revealed that Tom wasn’t “erased;” in fact, he had never been Thomas Veil, as that identity had been programmed into him in the first place. My theory is that the entire series is a prequel to Dollhouse, and that the Organization (or, at least, one of them) is an early version of the Rossum Corp who imprinted Veil but then had him go rogue. The series seems to show that Proto-Rossum is very good at imprinting people, but doesn’t seem to have figured out wiping them or returning them to normal lives afterwards.

Tom shows highly variable levels of competence and a wide variety of skills, some of which are more logical for a photojournalist to have than others. It’s not clear whether these bursts of competence are from his previous identity “leaking through” or from the mish-mash of skills that the Organization planted in him in the first place. Was he a dumbass imprinted with competence or was he competent and imprinted with dumbass? I’m inclined to think the latter, given that he originally was an FBI agent and which is why the Organization constantly underestimates him at key moments. Rossum never figured out that the meat mattered, not just the programming. This may include knowledge of how the Organization operates in the field, which accounts for his ability to consistently evade them but get captured by other groups.

Some episodes have the Organization specifically after Tom (to experiment on him), some have them specifically after the negatives, and a few seem to have unrelated weirdness going on. It stands to reason that there are, in fact, several competing conspiracies. Proto-Rossum needs the negatives back from their rogue test subject, but are also trying to test the limits of his conditioning. (Many of the higher-ups in this organization have all been imprinted with a certain personality/skill set, which tends to include a distinctive way of smoking cigars.) One competitor organization is trying to build their own imprinting tech and are trying to figure out how Tom works; others get interrupted by Tom’s investigations and figure out that Proto-Rossum wants him via corporate espionage. (The body-changer organization is the most prominent of these, and they also figure into the Hidden Agenda plot.) Various governmental organizations are also trying to get inside Proto-Rossum’s workings and vice-versa. The entire story is a mish-mash of corporate and governmental espionage.

Proto-Rossum is also stretched much thinner than it seems (especially outside of Washington DC); they’re good at laying traps but lousy at actually getting teams of people where they need them to be. They also aren’t good at tracking Tom at all; they seem to pretty much always catch up with him when he goes looking for elements of his old life, which makes sense, as they created those memories in the first place and know he’d end up in those places. Also, like any real-world organization, there are factions within Proto-Rossum with different goals and insanely complicated workplace politics. The fact that they skip perfectly good opportunities or make stupid blunders is explained by the workings behind the scenes, where the goals are different and the agents of the Organization are trying to sabotage each other.

Working grand theory about the Hidden Agenda plot: The government was going to pass a Homeland Security bill that threatened the undercover activities of both Proto-Rossum and the body-changers. The two companies came to an uneasy truce to deal with the situation: The body-changers would replace four senators, but Proto-Rossum would get photographic proof of the executions as leverage. Unfortunately, Agent Gemini also got those photographs, and hid his negatives. When Proto-Rossum caught him, they decided to use him for a different plot: To implicate the US military of actions in South America, while at the same time casting major doubt on his negatives (by giving him a doctored version of Hidden Agenda to work from) should he ever recover his memory and try to present them. At the last minute, changing political factions within Proto-Rossum caused the project to be shut down (Richard Grace discovered that the “Alyson Veil” he thought he was sleeping with was actually a body-changer company spy, and didn’t want to lose the Hidden Agenda leverage over that company). A poor cleanup meant Tom made off with the version of the negatives that wasn’t supposed to get out. For most of the series, there are factions within Proto-Rossum who want the negatives (to maintain their power over the body-changers), who want Tom to stop seeking the truth (because neither the South America fake story nor the dead senators real story is supposed to get out), and who want to test the limits of Tom’s fake memories (because they’ve never had this kind of stress-test before).

By episode:
101 Absolute Zero – Tom is “erased” when out to dinner with his wife. This episode introduces a number of recurring elements in the series, including a brief stay in a mental hospital (and various other patients Tom meets there) and the cigar-smoking affectation of many Organization higher-ups. While it might be tempting to believe nothing before the erasure is real (from the fact that the people in the restaurant change when he goes to the bathroom), it seems likely that Tom had to spend some time living his assumed life—if nothing else, he had to have really stashed the negatives rather than having memory of doing so programmed in, or the Organization wouldn’t have bothered planting them. Tom’s mother is later revealed to have been sick before he was erased—similar to the theory about his father later on, I think this woman was Tom’s actual mother, but long-estranged. The stroke might even have been a reaction to an attempt to imprint her with memories of being “Tom’s” mother.

102 "Turnabout" – Tom is able to sneak into a sanitarium when he’s mistaken for Dr. Bellamy, who he killed in 101. This turns into an elaborate trap for him as they enlist him in “breaking” a young woman who’s seemingly also been erased. Given that Veil and Bellamy look nothing alike and couldn’t even pass for the same age, the idea that “Bellamy” is an imprint that could be in a different body after his death would allow Tom to initially sneak in. At some point during the episode, the other people there get wise to the ruse and turn the situation into a trap for him. This episode provides strong fodder for the theory that Proto-Rossum can’t wipe, only imprint; and those imprints are very hard to overwrite.

103 "The Incredible Derek" – Following a magnified detail in his photograph, Tom hunts down a vehicle and army base connected to one of the conspiracies. Along the way, Tom encounters one of the few actual, possibly-supernatural events in the series, a blind clairvoyant boy named Derek. While Derek’s powers aren’t really explainable, it’s clear that Tom steps into the government program that Hidden Agenda was supposed to expose/influence (including a clearly-crazy former participant), and his poking around results in this section of it getting liquidated. Likely that this was, in fact, the American Guard from “Heart of Darkness” masquerading as the real US army for some purpose.

104 "Something About Her" – A pair of doctors attempts to reprogram Tom with memories of an actress as his lover, and overwrite the existing memories of his wife. Unfortunately, they get careless due to time pressure and the original memories re-assert themselves. This is some of the strongest evidence that there is a competitor organization that isn’t quite sure how imprinting works and are trying to duplicate it.

105 "Paradise on Your Doorstep" – A woman uses a photo of Alyson to lure Tom to a mysterious village, supposedly populated entirely by people erased by the Organization. I think there are two competing theories to what’s going on here: Either the village was set up by Proto-Rossum as a convenient holding pen for people they can’t wipe and/or a trap for Tom (they are trying to get the negatives, after all); or they are actually a group of people who were imprinted and then, for whatever reason, set loose. The former is the stronger theory—the chaos of the leadership change at the end meant the woman could have Tom returned to the outside before the Rossum higher-ups realized their man was no longer in charge. The latter theory implies that Proto-Rossum had tried to overwrite a large number of people and return them to normal life, but had failed and ended up with a lot of “erased” people searching for a life that never actually existed, eventually finding each other and forming a community.

106 "The Spider Webb" – While tracking a man he met in the asylum in 101, Tom is (very obviously) lead to the studio and writer of a pirate broadcast soap opera that is retelling events from his erasure. This, more than most episodes, very clearly must be a plot by Proto-Rossum to trap him, given how it requires clear knowledge of the events of his erasure (which they know), who he’d be tracking as a lead (which they know), and an in-depth knowledge of his behavior (which they have, they put it there). Theory: The sneering and pretentious writer Max Webb was imprinted with Veil’s imprint, plus sophisticated psychology and profiling skills, giving him near-perfect ability to predict Tom’s actions. Unfortunately, he got a bit of Tom’s short-sightedness and overconfidence in that mix, too. This is another case where it’s clear it’s not enough for Proto-Rossum to catch Tom; they need to break him psychologically enough that he gives up the negatives and the search. In this case, they were attempting to present their conspiracy as omniscient, all-powerful and inescapable.

107 "A Rough Whimper of Insanity" – Tom delivers pizza to a shut-in computer genius named Scott and befriends him. Scott is impressed by the extent of Tom’s erasure, assuming that the Organization has managed to thoroughly delete files everywhere. (Obviously, it’s not that they were deleted perfectly; it’s that they were never planted.) Eventually, he hunts down the Organization’s files and they use a very sophisticated VR system to access them, but after seeing Tom’s file (“It’s not what you think!”), the maladjusted Scott chooses to stay inside the system as it collapses, committing virtual suicide. Theory: Scott invented the brain-interface-computing technology used by Rossum in “The Attic”; he notes that he’d been living off the profits of a programming breakthrough that he sold to a startup years before, and the only people we ever see use this VR tech are Scott and his former teacher (who could have a setup from when she worked with him). [On an unrelated note, writer Joel Surnow’s lack of knowledge about both hacking and VR, and his complete disdain for computer geeks really shines through here.]

108 "The Alpha Spike" – Tom follows the trail of Dr. Bellamy to a private school where the headmaster is brainwashing the students into a perfectly obedient army. Obviously an off-shoot project of Proto-Rossum, as they immediately are interested in Tom when the situation gets escalated and they learn his real name. Probably a precursor project to the mind-linked soldiers in Dollhouse, intended to establish the same goal.

109 "You Really Got a Hold on Me" – Tom meets Gus Shepard, a man who claims to have been erased under similar circumstances to Tom’s 25 years earlier, who tries to convince Tom to give up and give the Organization what they want in order to get his life back; Shepard is miserable and ready to commit suicide. Instead, Tom convinces him that fighting the organization gives his life meaning, and gets him running again. I think the truth is revealed when Shepard says, “I’m you, 25 years from now.” The Organization imprinted Shepard with Tom’s imprint, plus 25 years of hiding and despairing and some false memories about acquiring information about Tom. (And they set up the self-destructing base as a setpiece, and sent in an actress to play the hooker.) They were hoping Shepard would convince Tom to give up and turn himself in. Obviously, this failed.

110 "Father" – Tom meets Jonathan Crane, a man who may be his long-estranged father (who left and was out of contact for 20 years; this episode also lets us peg Veil’s age at 37); except that the man changed his name years earlier, has had recent plastic surgery (around the same time Tom was erased), apparently underwent a personality change around the same time, and has no photos or memorabilia of Tom. Now, the twist in the episode is that Crane is in debt to some mobsters (which isn’t fully explained) and there is a photo of him and young Tom, fallen behind the couch. My theory is that Crane is, in fact, Tom’s father. Or more specifically, he’s the father of whoever Tom was before imprinting. The Organization took advantage of their estrangement, and when Crane went in for vanity surgery, they imprinted him with memories of having a different name and secretly following Tom’s photojournalist career (which he can’t supply any saved clippings from, natch).

111 “The Enemy Within” – Tom gets himself shot by the overzealous security guards of a farming collective and nursed back to health by a woman with a troubled but entirely mundane past. Nothing connected to any of the conspiracies happens, just a dispute between independent farmers and a corporation that wants to buy them out. The only point to this is to show that Tom can’t let go of his need to find out the answers of what happened to him; he can’t just settle down and be happy. (This was the only episode written by Peter Dunne, likely explaining the different tone from other episodes. Also, Tom was even stupider than usual.)

112 “It’s Not Such a Wonderful Life” – At Christmas, Tom notices a bundle of newspapers with Hidden Agenda on the cover and shortly thereafter is picked up by the federal government. They’re bringing “the organization” to justice and all they need is his testimony and his negatives. Alyson returns, claiming that she’s been on his side the whole time. Tom’s mother returns, recovered from her stroke and asking for forgiveness. It’s a perfect wish-fulfillment until Tom wakes up in the last two minutes to find the house ransacked, a videotape showing the arrests were staged, and a note from Alyson asking when he’d figured it out. This episode needed a longer explanation of its ending: Tom claimed to have gone out and gotten the negatives the night before, and seemed like he had fallen for the whole line and was going to hand them over, so why would the conspiracy ransack the house while he was asleep? Theory: This entire setup was by Proto-Rossum. Alyson works for them; Tom’s mother could have recovered and been properly imprinted in the interim. They faked the newspaper (thrown at his feet by an ominous van), the paparazzi, the TV broadcast (Alyson was with him when he saw it in a shop window—they could just queue it when they were scheduled to walk by) and the political setup. But like several other cases, they were on a deadline because they’re not as “all-powerful” as they seem. Perhaps the real Feds were about to close in on them. Alyson, under time pressure, opts to drug Tom and ransack the house rather than risk him holding out a few more days. When they can’t find the negatives in the house, she concludes he must have been stringing her along and never retrieved them, and calls the whole attempt a loss. Tom’s reaction (and the fact that the negatives were hidden in the house, just well hidden) indicates that Alyson shot herself in the foot—if she’d just been more patient, they would have won. (An interesting note at this point: Tom has said and thought virtually nothing about where and when he took Hidden Agenda, and what else he saw there. It’s interesting to wonder whether they did that intentionally to set the stage for the reveal in “Hidden Agenda”, or if they realized they’d been doing it unintentionally and took advantage of that.)

113 “Contact” – While trying to sneak into the archives of a photography company he’d submitted pictures to years earlier, Tom is contacted by a mysterious voice who claims to be an agent of the organization, looking to destroy them from within. The voice reveals that Richard Grace is responsible for Tom’s erasure, and had some kind of relationship with Alyson. Eventually, Tom is framed for Grace’s murder—which the conspiracy promptly covers up in the eyes of the public and the police. The voice then gives Tom a palmtop full of information on the organization, and tells him to work his way up. Theory: There’s no reason to believe this isn’t exactly what it seems to be. An insider wants to get out and wants to use Tom as a catspaw to do so. This fits with the theory that, rather than a unified, powerful conspiracy, Proto-Rossum is a mangle of bureaucracy and power-politics. We already know that Alyson is working for the organization, and whether she actually had an affair with Grace or that was all an act is really immaterial; it’s also possible that a fake Alyson from the company that appears in “Forever Jung” impersonated her and caused this situation while trying to sabotage Proto-Rossum. (It was also at this point that I realized Tom very rarely uses physical violence to get out of situations in the first half of the series; he ends up surrendering in a lot of situations where Number Six or an action star would have punched his way out. This changes as the series goes on, which might be a mark of character development as he gets more desperate, more of his original personality breaking through, or just a mandate from the network. In any case, this is pretty much the turning point where he stops acting like his life was erased last week, and starts acting like his been on the run for months and can’t trust anyone, so he needs to be clever.)

114 "Heart of Darkness" – Tom uses the palmtop to track down Commander Quinn of the “American Guard”, who appears to be the man who organized the execution in Hidden Agenda. He masquerades as a new recruit, in what appears to be a non-governmental pseudo-military terrorist organization, and demonstrates notably more competence than ever before. This is one of two episodes written by David Ehrman, and he’s marked as a Prisoner fan both by the more subtle psychological warfare he has Tom use, and by the drill sergeant labeling Tom as recruit #6. At the end, Tom gambles and is correct that the higher-ups in the organization do not want him dead, and is rewarded with Quinn’s assertion that the execution depicted in Hidden Agenda didn’t take place in a jungle, as Tom believes. Theory: It’s clear that Proto-Rossum has black-suited operatives who just do what they’re told and some kind of military presence; this may be where they’re coming from. Also, this is our first real revelation that Tom’s memories of Hidden Agenda may not match up to reality. There’s a slight possibility that there are people in the organization who do want Tom dead, but the voice from the previous episode intervened on his behalf.

115 “Forever Jung” – The palmtop give Tom an address for a nursing home, which he gets a job at and hears a cryptic rhyme from a senile resident. Turns out that the healthy old ladies are “dying” and being taken to a facility that makes them appear young again. What seems to be happening: Dr. Chasen takes women who won't be missed from nursing homes, alters them to look like other people, puts in a destructible implant, and after a certain amount of “training” (presumably a combination of physical training and brainwashing), sends them out to infiltrate and assassinate. Apparently Alyson Veil was altered in this way—or someone else was altered to impersonate her. For the second time in a row, Tom manages to bluff enough about his importance to prevent from getting killed, this time by mentioning "the director." It's not entirely clear what the implants do (they’re not entirely mind-control, because Pauline still acts to help Tom after hers is put in, but they may be related to it), but given Pauline's behavior at the end, they probably cause serious neural degradation when detonated--at the end, they physically changed all the women back as they stripped out the equipment, then detonated the implants so they’d all be senile and couldn't talk about what had happened. Theories: This could be Proto-Rossum, but there's no reason for them to alter appearances if they can imprint minds; they also wouldn't need the training or the implants. This is likely a competitor organization (who I refer to as the body-changers), who've built their own macguffin (the appearance-changer) and who, at some point or another, needed someone to impersonate Alyson Veil--who we've already established works for Proto-Rossum, so it would be for corporate espionage. This address was in the palmtop because Proto-Rossum eventually wanted to pull resources to investigate it. We could check back through Alyson's other appearances, as some of them might not be her--the affair with Richard Grace seems likely, for example. Tom's bluff about "the director" was just that--a bluff that worked because this organization is just as stupidly bureaucratic as Proto-Rossum. Also, there’s an implication that these operatives could only be used for short-term infiltration, because even if you start with a healthy 70-year-old, only changing her appearance and bone structure won’t get you a young woman, it’ll get you a young-looking women who’s likely to have a heart attack, or cancer, or senility.

116 “Shine a Light On You” – The palmtop sends Tom in search of a scientist who turns out to have disappeared a year and a half earlier, supposedly abducted by aliens. It turns out that the UFO lightshow was all a cover for a secret underground lab, where magnetic equipment is being used to perfect wireless energy transmission (which disrupts electronics and power transmission in the town above, and creates burn circles in the fields above the lab). Dr. Merrit “kidnapped” himself so he could work in secret, and tells Tom that he could have a happy life in exchange for just a “worthless photograph.” Tom opts to throw a metal medallion into the magnetic equipment and blow the place up in a shower of cartoon lightning. Theory: This is another competitor organization that Proto-Rossum was keeping tabs on, and given that Tom loves throwing around his real name, they were probably able to figure out that he’s the rogue project Proto-Rossum is in a tizzy over. Dr. Merrit has no idea what the photograph is or why Proto-Rossum wants it, but figures getting it couldn’t hurt his position. (Also: They never explain the flying UFO that’s seen in a couple of places, including two abduction attempts, but it seems likely that it’s a helicopter with a lot of fancy lights on it, that the scientists rigged up to help their cover.)

117 “Stay Tuned” – The palmtop sends Tom to a town in upstate New York, where everyone is just gung-ho about the local TV station and the new political candidate, Jim Hubbard. Hubbard has a distinctive birthmark on his neck, which matches the cigar-smoking officer in Hidden Agenda. Tom eventually puts together that the TV station is brainwashing everyone who watches it, except for one kid with vision problems and special glasses. So Tom pulls off his most brilliant ploy to date, deliberately getting himself caught by Hubbard so he can film Hubbard’s evil monologue, all while wearing contact lenses so he can avoid the effects of the TV but pretend to be a loyal soldier. Tom’s setup disables the mind control images and broadcasts Hubbard’s evil monologue instead of his planned stump speech, freeing the town and ruining the plan. Tom smirks at Hubbard as a cigar-smoking man in a black limo takes him away, but then sees a truck for the local TV station advertising that it’s coming to your hometown ,too. Theories: Hubbard confirms that Hidden Agenda wasn’t taken in a jungle, though Tom doesn’t seem to get more information out of him and doesn’t really try. Similarly, when the Organization picks up Hubbard, they make no effort to detain Tom. This is probably internal politics at work—Hubbard and the folks he works for have to be intertwined with Proto-Rossum in some way, because of the Hidden Agenda connection, but the direct superiors responsible for this project aren’t interested in Tom. (Tom’s mysterious contact may also be playing a behind-the-scenes role in protecting him.) I suspect that Hubbard is, in fact, a classic politician—mostly a power-hungry empty suit who gets involved in all sorts of projects (including Hidden Agenda and this one) without knowing what’s really behind them, and without really caring as long as he gets his. The mind-control TV plan seems like something Proto-Rossum would back-burner when they worked out more effective sound-based imprinting, because that’s easier to transmit and harder to avoid, especially as cell phones became common.

118 “Hidden Agenda” – Alexander Hale, the mole and Tom’s contact, has been found out by the Organization, and they implant him with a device that lets them see through his eyes and cause him pain remotely. He meets with Tom and encourages him to walk through his memories of taking Hidden Agenda, and then reveals that they’re all a lie. The episode ends with Tom visiting the real site where the picture was taken, a set within view of the Capitol Building. Theory: Obviously, the device used to see through Hale’s eyes was the same one used on Echo in “True Believer”. There were several clues throughout the episode that the memories shown are fake: The fact that Tom smokes like a chimney, the fact that everyone who could substantiate the story ends up dead, the fact that Tom is amazingly competent in ways he wasn’t for the first half of the series.

119 “Doppleganger” – Tom follows up on one last lead from the Palmtop, a photographer acquaintance named Claire Hillard who apparently covered some of the same military stories he did. It turns out that there’s another Thomas Veil who looks just like him and who manages to frame him for Claire’s murder. When Tom’s public defender concludes that Tom’s negatives are the perfect evidence to prove his innocence, Tom sets up his double to take the fall and flees town, discarding the Palmtop on the way out. Theory: Claire’s reaction to the print of Hidden Agenda before she was killed implies that she was connected to the Organization, and knew something about the events. The body-changer competitor organization from “Forever Jung” (who have a grudge against both Tom and Proto-Rossum for the loss of their facility, and may have connected it all to Hidden Agenda by this point) used their face-changing technology to create a fake Thomas Veil, and they were able to find out (via corporate espionage) what leads he still had from Proto-Rossum’s palmtop, so they created a life for fake Tom Veil and set up a studio for him to lay a trap. Taking out Claire in the process would be just another blow to Proto-Rossum. They may not know exactly what Tom’s negatives of Hidden Agenda are good for, but they know their competitor wants them very badly. Also, Tom isn’t a “pet project” of their “the director”, as they would have figured out following his bluff in “Forever Jung”, so they have no qualms about killing him.

120 “Through a Lens Darkly” – Tom is captured while watching an Organization dead-drop box and locked in house where he’s drugged and hypnotized into reliving memories of the violent death of his childhood sweetheart. When it seems like he’s broken, Tom smashes a camera and looks in the mirror inside it to relive one last memory: Of the woman encouraging his search for the truth. This snaps him out of it long enough to crash the car and escape. Theory: The “magical” events of this episode, including auto-locking doors, disappearing people and scene-shifting, are all just the result of drugs and hypnotism and we’re seeing Tom’s point of view. This episode is kind of a sequel to "Something About Her", as we have no reason to believe that the memories of Laura are real, or were present before this episode. (They need to be at least somewhat altered, give that Tom wasn’t a photographer in his real past.) The other thing we learn in "Something About Her" is that Tom’s mind fills in a lot of the gaps about his false relationship that aren’t directly programmed in scenes we see—which makes sense, as programming in an entire lifetime’s worth of memories seems prohibitively detailed. In this case, Tom’s mind created that last memory based on what his core personality wanted to believe had happened—his subconscious retroactively filled in events that would lead to his current personality existing.

121 “The Dark Side of the Moon” – While Tom is fleeing from a gun-toting Organization operative, his bag (and his negatives) are stolen by a gang member. Tom and the operative go on a grim and gritty hunt through gang territory, which would hold more pathos if it didn’t seem like every member of the gang had walked off the set of The Warriors. Tom retrieves his negatives but misses his appointment with a contact, and discovers that the mysterious voice on the radio who has been broadcasting cryptically-appropriate statements all night was a recording set up by something who smokes cigars. Theory: Sending a single man with a gun to retrieve the negatives is out of character for Proto-Rossum; if they were willing to do that, why not do it months earlier? One possibility is that one of the various competitor organizations, who don’t feel the need to play psychological tricks, sent this guy (who seems like a freelance mercenary, given how long they take to pick him up) and all of the other “connections” are just Tom and the audience being paranoid. The other is that the entire scenario—the operative, the gang, the girl, the voice on the radio, even the contact Tom is supposed to meet—is a setup by Proto-Rossum to try to break Tom’s spirit, to convince him to abandon the negatives and give up. That would better explain the more ridiculous elements of the episode, like the cockney gang leader, the fact that the girl was able to find him repeatedly when the gang couldn’t, the really long wait for the operative to get picked up, etc. This is the second episode written by Prisoner fan David Ehrman, which makes me lean towards “everything is a setup” as the intended interpretation. (There seem to be two types of episode resolutions in the back half of the season: “Tom is clever” and “Tom is determined.” I much prefer the former.)

122 “Calaway” – Tom discovers that he’s lost the ability to sleep, and the clues to his condition lead him back to Calaway, the mental hospital where he’d been taken just after his erasure. He discovers that Dr. Novik, the latest agent of the Organization trying to retrieve his negative, is actually another patient from his time there. When he manages to collect enough evidence to convince the man that his identity is false, they escape. Before going off to try to find a family he doesn’t remember, Novik reveals that Tom’s “neural architecture” has been rebuilt, and the insomnia is just the first sign of an inevitable collapse; and that the Organization has big, big mind-control plans that there’s no time to stop. Theory: Novik is obvious a false, imprinted identity. But nothing we see indicates that “J.C.” wasn’t false, also—he never talks to his wife, his daughter thinks her father is dead, and the only evidence of his previous identity comes from Organization files. Proto-Rossum, as noted before, doesn’t know how to wipe people, just imprint them, and the process isn’t long-term stable. (Given the regular checkups former actives need to come in for in Dollhouse, they may never have fully stabilized it.) So they decided to make J.C. useful by turning him into Dr. Novik, and they took advantage of Tom’s degradation as another opportunity to try to break him and get his negatives. (Note that the degradation has nothing to do with Tom’s initial stay in Calaway, but came from his imprinting some time before that. The location of Tom’s studio and house relatively close to Calaway, so that he’d end up confined there, may be because there’s a greater hub of Proto-Rossum operations in that area.)

123 “Zero Minus Ten” – Tom wakes up in a hospital, and is told that he’s been in a coma for three months and the events of the series never happened: It’s days before the gallery opening when Hidden Agenda was originally displayed, Alyson loves him, and his best friend Larry is alive again. Of course, with his friend’s help, Tom is able to uncover evidence that the coma was faked and recover memories that he was presumably drugged to blur. He discovers that he was in the hospital for only three days, and the negative was still in his locker at the printing plant he was working at a week before. When he calls her on it, Alyson reveals the bluff but also that she cannot (or will not) kill Tom. Theory: This episode gives us more evidence that Proto-Rossum has different political factions working at cross-purposes. Alyson works for them, and is an excellent actress, but is prone to giving up too early and not planning for contingencies. A separate faction—or more likely the body-shifting competitor organization—made a Larry that muddled her plans, so she got frustrated and killed him, dropping an earring in the process. Which was what eventually ruined the entire plan. (Though the Organization seems more willing to kill Tom in these last few episodes, no one actually goes through with it, even when given a clear opportunity. Which implies they aren’t actually willing to kill him, likely because of whichever faction considers this all a test of his conditioning.)

124 “Marathon” – Tom discovers a radio frequency in one of the other photos on the Hidden Agenda negative, and listening in on it clues him in to something called “Heritage House”. Turns out that Heritage House is an FBI operation to track the Organization, but Tom gets there just as the Organization takes steps to wipe them out. Tom eventually connects with FBI director Robman, who is able to discover that Tom’s copy of Hidden Agenda was doctored and one of the men in it is a US senator (who briefly disappeared a year earlier). Tom takes Robman to the real execution site, but when the secretary they’ve been protecting the whole time is revealed as a programmed sleeper agent, Robman gives Tom a safe deposit box key and sends him off, and neither of them knows who can be trusted. Theory: Robman believes the Organization to be a “private security company” with unlimited funding, not part of any government. You can make a very good impression of “unlimited funding” if you have several large cutting-edge biotech companies and a brainwashed paramilitary organization that all appear to be one conspiracy. The phone-triggered assassin state is a preliminary version of the “There are three flowers in the jar” trigger programming the Dollhouse used for November. (Please, don’t get me started on the Organization tracking a radio frequency and somehow sending feedback through it. Close your eyes and ignore the terrible science in that scene.)

125 “Gemini Man” – Tom opens the safety deposit box and gets the files and the key to the safehouse of an FBI agent named “Gemini”. After very cleverly avoiding the Organization’s attempts to take it from him, he discovers the true identities of the four US senators killed in Hidden Agenda, and goes to the fifth member of their committee for help. That man is eventually turned against Tom when he goes to the #2 man in the FBI, so Tom tricks that FBI man into leading him to the Organization’s repository of information about Gemini. Most of it has been deleted when Tom gets there, but he still learns the truth: Tom is Gemini; Thomas Veil was never real, and was programmed into him by the Organization. This entire endeavor was (at least in part) to test the limits of this programming.

My take on an epilogue: From what we see in Dollhouse Season 2, Rossum is still working to keep their agents stable in the upper tiers of government, so obviously there were some setbacks. While the computer files on Gemini had been wiped, there were still some unshredded paper files, additional video tapes, and shredded but not destroyed files that could be reconstructed. Tom probably filled his car with everything not nailed down, took it all back to Gemini’s safehouse, and stayed there for a month coming to grips with himself. Then he went back on the road, because he’s on the clock (eventually his brain is going to collapse) but he has a giant collection of tapes and probably a few files on other brainwashed agents--He has a collection of likely allies. They eventually manage to expose the body-changers and a few of Proto-Rossum’s agents, as Tom learns the limitations of their programming/disguise techniques, resulting in a massive purge of the FBI and several senate retirements that are largely kept secret from the public. Five years later, a terrorist attack on the World Trade Center allows the Homeland Security bill to go through, and the enhanced governmental powers allow them to destroy most of the American Guard…but by this point, Rossum has cut ties with them and set up their first batch of Dollhouses, having stabilized the active architecture enough to wipe and safely overwrite memories.

Tom likely goes out in a blaze of glory, getting shot or blown up just as a masterstroke goes into effect, such as detailed files and photographs—possibly including the diary that is the framing device of the series—appearing on the desk or monitor of every high-ranking intelligence officer in the country.
The files regarding this entire story as sealed and hidden, which is a shame, because they could have been very useful to Agent Paul Ballard.
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