The TARDIS materialises on Mars in the 22nd century, and the Doctor, Fitz and Anji visit the New Jupiter café in Sheffield -- where two off-duty military personnel suddenly attack Anji for no apparent reason, putting her in hospital with a skull fracture. Her attackers are shipped off to Earth for unspecified treatment, and the Doctor, disturbed, traces their previous assignment to Farside Station, a military installation in orbit around Jupiter. He and Fitz fake credentials as Earth Force accountants and travel to Farside to investigate. While Anji recovers and waits for her friends to return, she sees a television programme about old-style capitalist trading methods, and writes in to complain about the inaccuracies, netting herself a job offer as a consultant once she is checked out of hospital. She strikes up a friendship with the cameraman, Michael, but doesn’t expect anything more to come of it... until word reaches Mars that Farside Station has been lost with all hands. The Doctor and Fitz will never return, and Anji is stuck on 22nd-century Mars in a life that no longer feels like her own.
With no other option, Anji carves out a new life for herself, starting off as a consultant for the network and moving on to bigger and better things. She and Michael continue their relationship, and eventually marry; Anji works hard and plays hard, and makes sure to keep up on all of the latest vaccinations, ensuring that she rarely falls ill. However, every time she sees Jupiter or is reminded of Farside’s loss, she remembers that this is not her real life, and feels the urge to find out what really happened. She begins to correspond with the families of those lost on Farside, and hears rumours that the military has hushed up the discovery of a janitor’s charred body, found in an escape pod and identifiable only by his DNA. Meanwhile, a new military unit known as the Professionals makes its presence known in Earth space; when Anji’s workplace is attacked by native Martians demanding independence, the siege is broken by the space-suited Professionals, who show no concern for anything other than their job and certainly display little care for the Martians’ hostages.
One of the Professionals is causing trouble for Colonel MacNamara, the man in charge of the programme; his people have been unable to erase this subject’s core personality completely. During a field exercise, MacNamara orders his troops to open fire prematurely, driving alien rebels out of their homes and towards this particular Professional -- but he only kills one of them, a young man who got caught in the magnesium fires and would otherwise have died slowly and painfully. MacNamara decides to have this Professional terminated, but before he can sign the orders, he learns that the Charing Cross has detected Farside Station, which is intact after all and is now orbiting within Jupiter’s atmosphere. MacNamara decides to send the troublesome Professional to find the secrets of Farside -- or die in the attempt.
By this time, four years have passed since Farside was lost, but Anji is still haunted by a powerful urge to find out the truth, which is causing some tension between her and Michael. The urge resurfaces when she sees a news report about unusual weather patterns on Jupiter; she subsequently learns of the Professional’s mission through her contacts, and bribes O’Connell, the pilot who has been hired to fly the Professional to Jupiter, to let her tag along. O’Connell pilots the Professional into Jupiter’s atmosphere, and the Professional then leaps out of the shuttle, relying on his suit’s servo-motors and hydraulic grappling hooks to get him to Farside. He is unaware that Anji is following him; O’Connell allowed her to hide in the auxiliary fuel tanks and provided her with circuitry that linked her suit to the Professional’s, allowing her to copy his movements.
The Professional and Anji touch down on Farside, which is covered with a strange sort of rust. Anji tries to avoid the Professional by entering through a different airlock, but finds him waiting for her; his personality is completely subsumed to the requirements of the mission, and although he was unaware that there was anyone following him, he doubled back to check just in case. Anji tells the Professional that she’s here to find out what happened to her friends, Dr John Smith and Fitz Kreiner. The Professional, recognising her from the TV news, decides that she’s telling the truth, and confirms that her friends were on the passenger list of the PSV Pegasus. They presumably reached Farside alive -- but from the condition of the station, it seems unlikely that anyone could have survived here for four years.
Four Years Earlier: As the Pegasus nears its destination, its pilot goes berserk and flies directly into Jupiter’s atmosphere while repeatedly stabbing himself with a harpoon. The Doctor tries to reason with him, but the pilot fires the harpoon into the Doctor’s abdomen; only the Doctor’s quick reflexes save him from serious injury. With the help of Captain John McCray of the 101st Airborne, the Doctor seals off the cockpit and fires it into space; the pilot will survive to be picked up later, and McCray can safely guide the ship in to dock from auxiliary control. On Farside, McCray is reunited with the rest of his squadron, and the Doctor and Fitz meet Commander Jennifer Valetti. The Doctor hides the extent of his injury, hoping that it will heal without his having to seek medical attention; in this era, there could be fatal consequences should the human race discover an alien amongst them. Nevertheless, the pilot’s inexplicable breakdown seems to confirm that whatever caused the soldiers to snap on Mars is related to Farside, and since one of his friends has been hurt, the Doctor is determined to find out whether the incidents were accidents or deliberate tests of a new weapons system.
The next morning, Valetti provides the Doctor and Fitz with security passes and gives them a tour of the station. This is where human scientists work on technology to prevent another alien attack like the one Earth recently suffered; projects include an attempt by Professor Deschamps to create artificial singularities. Despite Valetti’s talk of pulling together, Fitz notices that the scientists and military don’t regularly mix with the station’s support staff; the Doctor, for his part, notices that level six isn’t officially drawing any power from the reactors. In order to cover his real agenda and look for more evidence, the Doctor sets up a software programme called AuDoc, capable of learning and independent thought, to scan the station’s finances.
Fitz visits the cargo bay, which is nicknamed “Greenwich,” since it’s the station’s exact midpoint. There, he accidentally bumps into a man named Archer, causing him to spill the parts he’s carrying. Archer’s supervisor, Robertson, is impressed when Fitz chips in without complaint to help clean up the mess he’s caused; however, he warns Fitz that if he breaks something, he’s off the team. As they work, they see the 101st bringing in the cockpit from the Pegasus and sedating the still-crazed pilot -- a job that should technically be under Robertson’s jurisdiction. As the pilot is taken for treatment, a station janitor begins to clean the residue of Jupiter’s atmosphere off the Pegasus’ hull.
Now: The Professional leaves Anji sealed in the airlock without her spacesuit, but she unexpectedly passes out and wakes to find herself locked in a cage, surrounded by feral men and women. She is released by the wary Joshua Easter, who explains that his men found her, vented the air until she passed out and brought her in for questioning. “Greenwich” has been transformed into a shantytown locked down behind an electric fence; the survivors are all on edge, and the hostile Caroline Arquette accuses Anji of collaborating with the enemy. Anji learns that a patrol led by Robertson has been sent out to follow the Professional, and warns Easter, who’s never heard of the Professional Unit, that this is a mistake that could get them killed. Even as she tries to warn them of the danger, the Professional turns on his stalkers and begins to pick them off, and Easter allows Anji to contact him and inform him that he’s shooting at the surviving station personnel. The Professional stops firing and orders his attackers to drop their weapons, but although they do so, electrical engineer David Verger has already been shot through the chest.
The patrol returns to Greenwich, but Easter refuses to speak to the Professional until he’s stabilised David’s condition. The Professional explains that he’s an Earth Forces special operative under instructions to treat any contact as hostile until proven otherwise. Robertson recognises Anji’s name, and confirms that her friends were on the station when it fell, although he never met the Doctor in person. The survivors then ask about the progress of the war, convinced that they were attacked by aliens and that a blockade has prevented Earth Forces from coming to the rescue. The survivors claim that, after a number of mysterious incidents, the station went on red alert, the air pressure rose dramatically, and the hub was cut off behind an impenetrable energy barrier. The survivors on the rim found a charred body at the bottom of an elevator shaft, identifiable only by his DNA as the janitor Jason; fearing possible contamination, they expelled him into space in an escape pod, but before anyone else could leave, the Station dropped into Jupiter’s atmosphere. The support staff have been scrambling to keep their home in one piece ever since, impeded by attacks from monstrous aliens whose touch drives their “Wounded” victims mad. The Professional confirms that he’s been sent to determine the viability of a full rescue mission, and privately warns Anji not to get too close to the survivors. Though they claim to have been fighting alien aggressors for four years, they have suffered no fatalities, there’s no immediate sign of an alien presence on the Station, and as the Professional and Anji both know, Earth is not at war. The Professional believes that four years of constant struggle and trauma, with no hope of rescue, have driven the survivors mad.
Four Years Earlier: The Doctor learns a great deal from AuDoc’s analysis of the station’s finances, and Fitz learns more from chatting with Robinson. Earth was recently occupied by aliens, and the atmosphere on Mars is still suffering from the effects of a counter-terraforming virus. Humanity has become scared and paranoid, expecting another attack at any moment. Fitz has also learned that the 101st has been bringing in cargo, a job that should be assigned to Robinson’s team. The Doctor confirms this through AuDoc, and discovers that the shipments are linked to a project being run by station psychologist Sara Mukabi and her husband, computer technician Terrance. However, AuDoc begins to slow down as the Doctor makes more demands on it, indicating that something else in the network is drawing too much processing power.
The Doctor visits Recreation Hall A to speak to Valetti, and finds her performing with a string quartet. Genuinely impressed by her skill, he then learns that the cellist was Terrance Mukabi, and asks for an introduction. Valetti invites the Doctor to dine with them, and the Doctor notes that the wine was shipped to Farside in bottles designed to replicate cellar conditions. Sara explains that this is part of her research; she works on ways to make people psychologically comfortable in environments entirely unlike those they evolved in. Sara jokes about her previous marriage, to a man who is now an admiral, and Valetti brings the conversation to a close after telling the Doctor that the Station was built in this area for security reasons.
Fitz visits the crew’s mess hall to share a beer with Robertson; on the way, he spots Archer working at a wall outlet. McCray is also at the mess hall, but while he and Robertson are old friends, McCray spends more time with his men; the 101st have a strong bond, as they are one of the few national units to survive the fundamentalist jihads and the alien invasion. Fitz realises that Robertson is besotted with computer engineer Caroline Arquette but is too shy to make a move -- and to Robertson’s horror, Fitz sits down next to Caroline and tells her that his friend would like to buy her a drink. To his delight, Robertson and Caroline hit it off at once.
The pleasant night out is interrupted when the Pegasus explodes in the docking bay. Valetti orders the crew to seal the bay and vent its atmosphere into space before the fire hits the station’s fuel lines; however, the Doctor spots movement, and leaps into the bay as the bulkheads close. After the atmosphere is replenished and the bulkheads are reopened, however, Fitz and Valetti find that the Doctor survived by sealing himself inside an emergency cupboard with the man he rescued -- the janitor, Jason. The strain has reopened the Doctor’s wound, which isn’t healing as quickly as his injuries normally do, and as he returns to his quarters to rest, Fitz worries that the amnesiac Doctor may not have known what he was doing when he leapt into the docking bay. Fitz returns to the docking bay to help Robertson clean up, and finds that Caroline has also volunteered. In the debris, Fitz finds Jason’s ID tag, which indicates that he is John McCray’s older brother. Robertson claims that McCray rarely talks about Jason these days, since Jason suffered some sort of accident that rendered him incapable of processing language. However, Fitz also finds a book of poetry, and notices that the handwriting matches Jason’s signature. Meanwhile, the station goes to Defcon 4 status until the investigation into the explosion is complete.
Now: Anji and the Professional wait for nightfall and then slip out of the compound, past the automated defences, to find out the truth. Once past the defences, however, they are attacked by hostile aliens who force the Professional and Anji away from the compound towards the energy barrier around the hub. The Professional holds off the aliens with laser pulse mines while he downloads data from the station’s computer system; however, one of the creatures gets through and forces the Professional up against the barrier, damaging his suit. The Professional drives the alien back and shoots open a fuel conduit, forcing the aliens to retreat; he and Anji are protected by their suits, however, and crawl through the burning fuel line back into the compound. There, the villagers are scrambling to prevent the explosion from tipping the balance and causing the Station to fall further into Jupiter’s atmosphere; once they have vented the fuel from the line, the Professional and Anji emerge, safe.
Although fully aware that the human race is not at war, the Professional decides to let the survivors continue to believe this is the case so that he can use them for his own purposes. Robertson and Easter now reveal that they were forced to strip all of the station’s escape pods just to keep Farside from falling apart around them; there’s no way off without help from outside. They realise too late that the Professional is manipulating them, putting them in a position where it seems that they’ve given up hope and that only the Professional can save them. Caroline buys into it, and the disgusted Easter passes on command, letting her take charge.
The Professional orders Anji to have Robertson recover the data he downloaded. Robertson is furious with the Professional, but sympathises more with Anji, who explains that she’s been cut off from her home and family and came here because she was desperate to find out what had happened to her friends. She also tells him that nobody knows who the Professionals really are; they could be robots, the resurrected dead, or alien prisoners brainwashed to fight for Earth. Robertson finds that the data from the station computers is riddled with corruption, and he and Anji give it all to the Professional, hoping to keep him busy. While doing so, Anji sees that the Professional is wearing an implant that releases chemicals into his body to relieve pain and keep him focussed; when he’s not looking, she steals one of his refills. Meanwhile, the Professional, still haunted by memories of the burning young man he once shot, tries to put these distracting feelings aside by using his release valve, a journal in which he records his innermost thoughts.
Four Years Earlier: The Doctor analyses the docking bay’s surveillance footage and finds that Jason may have accidentally transferred some of the atmospheric residue from the Pegasus to the cover of his journal. He already believes that Valetti lied when she told him why the Station was built near Jupiter, and he has learned that Sara Mukabi once served on a science mission to Jupiter that ended when most of the crew suffered inexplicable nervous breakdowns -- and, through AuDoc, that the Mukabis are responsible for a number of secret expeditions into Jupiter’s atmosphere. Fitz impulsively asks AuDoc to look for any signs of unusual activity that might be alien-related, telling it to use its initiative and join the dots. He then sets off to fetch equipment with which the Doctor can analyse the stain on Jason’s journal. While doing so, he meets the irascible Professor Deschamps, who complains that his singularity project is in jeopardy because Terrance Mukabi has neglected his computer-repair duties. As Fitz leaves Deschamps’ lab, the test rats in the corner suddenly become violent.
The Doctor checks on Jason in the station’s sickbay, and discovers that the janitor has a cranial implant. Valetti catches him, and has little choice but to show the Doctor the rest of the secret project. She upgrades his security pass and takes him to the Avatar chamber on Level 6, where he finds that the Mukabis have given every member of the 101st an implant like Jason’s. Since the project is being run by a computer technician and a psychologist, the Doctor easily deduces that they’re creating a military training simulator that tricks the mind into believing that the events it’s experiencing are real. The level of detail in the simulations is eating up processing power on the computer network, explaining AuDoc’s sluggish performance earlier. The Mukabis are also using the technology for non-military purposes, such as modelling Jupiter’s weather patterns for the next 10,000 years. However, despite their apparent openness, the Doctor notes that one door in the chamber remains locked.
Fitz later theorises that the Mukabis are trying to create a private army of mind-controlled soldiers. The Doctor explains that this project is top secret because the aliens who used Earth used similar technology to control their human slaves. He suspects that the rats’ violent behaviour is a red herring, and that they were simply reacting to the space-time pressure caused by Deschamps’ singularities. Convinced that there’s more to the Avatar programme than he’s been shown, the Doctor sets AuDoc searching for equipment discrepancies, while Fitz visits the mess hall to speak with Robertson. He is happy to see Robertson and Caroline sitting together, but less pleased when they reveal that the station has gone up to Defcon 3 due to rumours that alien ships have been spotted on the edge of the solar system.
Now: Despite Robertson’s pleas, Caroline throws in her lot with the Professional, who believes that the aliens must be travelling to and from their ship via an interstitial transit vortex. With the villagers’ help, he intends to lure the aliens into a trap, trace them back to their base on the station, and use their intertrix to escape. Meanwhile, Anji meets Toby, a three-year-old boy whose father is behind the energy barrier and whose mother is Wounded. While Toby plays join-the-dots games on the only surviving computer pad in the station, Easter reminds Anji that the Wounded won’t be able to fight; even if the Professional’s plan works, they’ll have to leave the Wounded behind. David Verger’s condition is deteriorating, and Anji gives Easter the vial that she took from the Professional; Easter analyses its contents, but concludes that they are keyed specifically to the Professional’s biochemistry. Disturbingly, the chemicals appear to affect the way the Professional thinks -- and in order for them to work, the Professional must have had seriously invasive neural surgery at some point.
Four Years Earlier: While the Doctor analyses the residue on Jason’s journal, Fitz inadvertently makes a comment about the Doctor’s past -- and the Doctor admits that, while he still can’t remember who he was, he knows that this is where he belongs. Fitz then mentions that he’s set AuDoc to scan the station’s computer for unusual activity, and the Doctor shuts it down, warning Fitz that it might take his instructions too literally and try to break into the secure systems, thus alerting the crew to their activities. However, he finds that AuDoc has picked up evidence that biohazardous material is being shipped into the Station. It also reports that maintenance has filed a high number of overtime requests, which causes Fitz to wonder: if Robertson’s crew isn’t responsible for maintenance, then what was Archer doing at the wall panel earlier?
Sara Mukabi then summons the Doctor and Fitz for a psych profile test, claiming that she needs more input for the Avatar simulations. When asked what animal he’d like to be, the Doctor chooses a unicorn. He inquires about Sara’s interest in Jupiter’s atmosphere, and she explains that the members of her previous expedition were affected by a substance that heightens the fear response in the human brain. The 101st have been collecting samples of the substance, Nightmare, which she has been using to enhance their experiences in the Avatar simulations. This is the real reason she used the system to model Jupiter’s future weather patterns. Still dissatisfied, the Doctor tries to break into the sealed chamber in the Avatar room, but Valetti catches him doing so and this time refuses to tell him what she’s hiding. He realises that she doesn’t really like the Avatar project, but she insists that, as distasteful as it is, Colonel MacNamara’s Professionals programme is worse.
Valetti admits that she likes the Doctor, and that she’s sent word back to Earth to ensure that he and Fitz will be immune from prosecution if news of this project becomes public. The Doctor realises that this means he and Fitz will soon be exposed as fakes, and returns to their quarters to warn him; however, they find themselves locked in, and the communications unit explodes, breaching the hull. The Doctor wraps himself and Fitz in thick blankets and creates a makeshift oxygen bottle from the equipment that he was using to analyse the substance on Jason’s journal; however, he only has enough material for one, and Fitz volunteers to go without, knowing that only the Doctor will survive exposure to space long enough to drag them around to the airlock. The Doctor carries Fitz to safety, and while Fitz is patched up using a ReGene machine, the Doctor tends to his own injuries and then erases the machine’s memory so it won’t report his alien physiognomy. Furious that another of his friends has been harmed, the Doctor confronts Valetti and provokes her into challenging him to outwit the Avatar programme -- a challenge he promptly accepts.
Now: As the Professional had planned, the survivors lure the aliens into a trap and plant a tracker on one, but the aliens’ retreat takes them through a damaged area of the station, exposed to high levels of radiation from outside. Robertson tries to convince Caroline that entering this area is an automatic death sentence, but she can no longer see beyond the fight -- and when Robertson points out that the Professional and Anji are protected by spacesuits, the Professional deliberately removes his, showing the survivors that he’s willing to face the same risks as they. Realising that he’s lost, the enraged Robertson snaps and leads the charge into the high-radiation zone, driving the enemy back until they reach the aliens’ nest... and there, they find no sign of an intertrix or teleport. All they find is a ReGene machine that the enemy have clearly been using to patch themselves up after each skirmish. Robertson orders the survivors to take the ReGene unit back to the village; stunned by the failure of the escape plan, Caroline does not argue with him. Neither does the Professional, whose painkiller vials were damaged in the battle. As the villagers return to Greenwich, demoralised, Anji discovers that one of the aliens scratched her during the battle; she is now doomed to become Wounded.
Easter puts David into the ReGene machine and sets it to its default mode; it will scan his DNA and patch up the damage to his body. Meanwhile, Anji checks the surveillance footage that the Professional had recovered, and finds an image of Fitz trying to beat out the flames on a man’s body; however, she feels nothing when she sees this, as if it is an image from another life. She suggests to Easter that the singularity project may have created a zone of quantum uncertainty around the hub; if so, perhaps inside the hub they can change the past and prevent any of this from having happened. Meanwhile, the Professional orders Robertson to repair his medication dispenser, and while doing so, Robertson accidentally triggers the Professional’s journal and hears one of his entries. The phrasing reminds him of Jason McCray’s poetry, but the Professional looks nothing like Jason. Without his medication, the Professional is becoming distracted, and has become obsessed with the corrupted data in the download, convinced that he can see patterns in it. Seeing this, Robertson finally accepts after four years of struggle that there’s no rescue coming and that the people of Greenwich Village are doomed.
Four Years Earlier: Valetti has second thoughts about accepting the Doctor’s challenge, but Terrance Mukabi convinces her that this could be a good chance to test their non-invasive procedures. Meanwhile, the Doctor visits Fitz in sickbay and gives him a data chip, telling him to install it at a precise time; the Doctor intends to push the Avatar simulation to its limits, drawing so much processing power from the network that AuDoc will be able to break through the security firewalls and find the information the Doctor needs. Much of his effort will be expended in convincing the simulation that he is human. The Doctor is connected to the programme and run through a few tests, and the Mukabis, impressed by his quick reflexes and talent for improvisation, decide to put him in a simulation of the Achebe Gorge battle on Mars. Rather than fighting as the historical Marines did, the Doctor rushes forward and draws the Martians’ fire -- causing his attackers to shoot out the cliff, which collapses atop them, enabling the 101st to win the battle. Previous simulations had considered a mere 80% survival rate a success. The Mukabis then order the 101st to hunt the Doctor through an asteroid field, but again, the Doctor turns his environment against his attackers -- and as the asteroids begin to crash into each other and explode, the simulation draws more and more processing power from the rest of the station.
Fitz runs into trouble when Archer is wheeled into sickbay, having burned his hands while working on a comms panel. Fitz manages to distract him and install the data chip, but he notes that Archer is himself trying to hide a data pad; however, Archer catches Fitz trying to find out what he’s hiding, and threatens to kill him if he pries further into Archer’s affairs. The station’s defences then unexpectedly open fire on Jupiter, and while the staff are distracted, Fitz retrieves his data chip -- only to see a message, apparently from AuDoc, warning him that it’s time to run. Down in the Avatar chamber, the Mukabis are forced to cut the simulation short due to the incident; it appears to be the result of a computer malfunction, but to avoid panic, Valetti announces that it was a readiness drill. However, once the Doctor has recovered from the strain of the simulation -- which has caused his abdomen wound to re-open -- he confronts Valetti, having realised that the 101st showed no sign of fear and were acting as if their minds had been linked together by the cranial implants. The Doctor warns Valetti that such invasive procedures could leave the 101st open to external influences, but Valetti refuses to listen and kicks him out of her quarters -- and then orders C&C to check the computers for any signs of tampering or sabotage.
Fitz gives the Doctor the files that AuDoc recovered, but they’ve been corrupted, as if AuDoc was attacked by another programme. Sara Mukabi then summons the Doctor and Fitz to the Avatar chamber, and when they arrive, they find that the locked door standing open to reveal an operating theatre. The Doctor finally realises that in order to fight aliens, the 101st must be trained to understand the aliens’ mindset; behind the shutters in the operating theatre are the preserved bodies of alien prisoners, kept in suspended animation at the moment of death so their latent neural energy can be tapped to provide the simulations with convincing enemies.
Sickened, the Doctor confronts Sara, and reveals that he’s learned that she was once married to Admiral Jonathan Ferguson, the man who arranged for Farside Station to be built above Jupiter; if she’s pulling strings for the sake of her research, is she cutting corners as well? But Sara pulls a gun on the Doctor, revealing that his psych profile is completely alien in nature. Valetti and the 101st arrive to restrain the Doctor, who tries to trigger a failsafe programme he planted in the computer to give himself and Fitz time to escape; however, security has found and removed it, as they’ve been watching the systems carefully ever since Fitz accidentally caused AuDoc to breach the firewalls. Valetti now accuses the Doctor of stealing classified files from the computer and sabotaging the Station, and although he claims that he’s not responsible, she orders Sara to strap him down and begin operating.
Now: Somehow, an alien gets into Greenwich Village, smashes the ReGene machine and flees for the barricades, where it recoils upon touching the rusty wire. The Professional hesitates before shooting it, and it knocks him aside and heads for young Toby; however, Robertson sees a particular scar in its flesh, and tackles it before Caroline can shoot it. The “alien” is David Verger, who has somehow been transformed into a monster by the ReGene machine. Robertson has David locked up, refusing to let a single person die after having survived for so long, but he knows that Caroline lost all hope in the future ever since she found out that she was pregnant but would miscarry due to radiation exposure and malnutrition. The Professional tries to convince the villagers to re-route power to the Station’s external sensors so that they can find the aliens’ supply ship, but Easter refuses, as this would knock out power to the barricades. The Professional attacks Easter, but Robertson knocks him out and orders the other villagers to lock him up. Caroline protests, but Anji now reveals that, although she played along with the Professional at first, there is no war, there never has been, and nobody’s coming to rescue them.
While the stunned villagers try to cope with this revelation, somebody gives the Professional’s computer pad to Toby, to replace the one that was damaged when the mutated David tried to flee. Caroline confronts the Professional, demanding to know why he lied to them, but he realises that she still needs to fight and convinces her to help him escape. Soon afterwards, Anji is found lying dazed by the outer airlock, and she claims that the Professional and Caroline attacked her and stole her spacesuit. While she recovers, Easter finishes repairing the ReGene unit and finally gets around to analysing her blood in order to find out when she will become Wounded. However, he finds that something else has already infected her, that the infection has rewritten her neurochemistry and her immune system -- and that there’s no sign of any physical damage to her body, which implies that Anji wasn’t attacked as she’d claimed.
The Professional and Caroline return to the village after setting up the station’s external sensors, and deny attacking Anji. Before Robertson can lock them up, the aliens attack the village in force, and the villagers run to man the barricades. The Professional and Caroline find Easter lying unconscious but dismiss him for the moment. Too late, Caroline realises that the Professional still intends to complete his scan, although this will mean that the aliens overrun the barricades. When she protests, the Professional knocks her out and activates the sensors, drawing power from the barricades and allowing the aliens to enter Greenwich; however, the scan reveals no sign of any alien spacecraft in the vicinity. Unable to think clearly, the Professional happens to catch sight of the computer pad, which Toby has dropped. The Professional had been analysing the corrupt signals from the data core, but Toby has joined the dots in the static to create a picture...
Four Years Earlier: While Sara analyses a sample of the Doctor’s blood, the Doctor tries to convince Valetti that the Earth she believes in isn’t one where alien prisoners can be tortured, and that Sara has cut potentially dangerous corners while conducting her research. Valetti, hurt by his betrayal, refuses to listen to him, but then the Doctor’s restraints unexpectedly click open and the lab’s intruder defence systems open fire, forcing the soldiers under cover while the Doctor and Fitz flee. The Doctor realises that something is trying to protect him, and he thus gets to a computer terminal, analyses Sara’s work, and discovers that his blood contains an alien infection -- which is why his wound hasn’t healed. When the pilot of the Pegasus stabbed himself and then shot the Doctor with the same harpoon, he passed on something from his own blood. The Doctor wonders why the infected pilot tried to destroy the Pegasus in Jupiter’s atmosphere, and while he runs a scan, Fitz notices another programme running on a nearby console; before he can draw it to the Doctor’s attention, however, the 101st arrive and recapture them.
Valetti questions Robertson, who is shocked to learn about the Doctor but insists that Fitz seems to be a genuinely good person. The frustrated Valetti leaves for a moment, and Robertson slips into the brig to speak with Fitz; he doesn’t see the Doctor, who is lying in a corner of the cell. Fitz recalls that Robertson told him that people on his crew get transferred away if they break things, and when he asks, Robertson confirms that the two soldiers from Mars and the pilot were exposed to a sample from Jupiter’s atmosphere when they accidentally dropped a capsule in the cargo bay. Valetti then returns and sends Robertson back to work, while the Doctor and Fitz are taken to the lab for further study.
Security is working to clear AuDoc out of the computer systems, but the Doctor has now worked out the truth. Deschamps’ experiments have nothing to do with the problem, and the files that Valetti accused the Doctor of stealing were actually stolen by Archer. The substance that Sara has named Nightmare is a refined version of something in Jupiter’s atmosphere, which infected the two soldiers and the pilot when they were exposed to a sample. When the Mukabis modelled 10,000 years of weather in their computer, the virtual version of the substance evolved inside the simulation -- and escaped into Farside’s computer networks. The recent maintenance overtime is due to glitches caused by the virtual virus exploring its surroundings, and the virus released the Doctor from the laboratory because Sara’s analysis had detected its biological counterpart in his blood.
Valetti orders the Mukabis to hook the Doctor up to the Avatar system through Jason McCray’s implant in order to screen out any duplicity. The Doctor plays along, hoping to be proven innocent so that he can convince Valetti of the truth. However, just as the Mukabis are about to start, the programme that Fitz had noticed earlier finishes running -- and a power surge overwhelms the simulation, linking the Doctor directly to Jason’s mind and causing him to experience the same crippling overdose of fear that destroyed Jason. John McCray and the 101st suddenly turn and walk out of the laboratory for no apparent reason, and the Mukabis discover that the computer systems have been hacked. Another power surge causes the laboratory equipment to explode, and the Doctor and Jason are engulfed in the flames. Fitz tackles Jason and smothers the flames, but the burning Doctor staggers into an open lift shaft and falls out of the hub. The air pressure in the rim suddenly increases, and the stasis fluid keeping the alien bodies intact becomes volatile and erupts out of the containers. The burning Doctor hits the bottom of the lift shaft as the stasis fluid expands, filling the hub of the Station and then freezing solid...
Now: When the Professional sees that the dots in the corrupted files form the picture of a unicorn, he remembers who he really is -- and realises that Anji should have recognised him. He’s realised this almost too late, but before Anji can shoot him, Robertson arrives and knocks the gun out of her hands. Anji retreats to the barricades and leaves the village, and the aliens follow her, as they recognised the infection in her blood when she was scratched and only attacked the village in order to collect her. Anji had never expected to find the Doctor or Fitz alive; she came to Farside with another agenda, and has only now worked out what the agenda is. Meanwhile, back in Greenwich Village, the Professional introduces himself properly to Robertson and Easter; his memories have returned, and he now knows that he’s the Doctor.
The Doctor restores power to the barricades and explains the truth. Their real enemy is a biological weapon that’s been lying relatively dormant in Jupiter’s atmosphere for millennia; for convenience’s sake, the Doctor refers to it as Fear. Before humanity had even evolved, Jupiter was used as a testing ground for biological weapons by an alien race, and ever since then, two viruses -- Fear and Loathing -- have been waging war in the planet’s atmosphere. The experiments on Farside broke the deadlock by creating an artificially evolved, virtual version of Fear, which found a way to take over the Station and turn it into a weapon for use against its enemy.
The pilot of the Pegasus, infected by Fear, was trying to destroy a pocket of Loathing; some of that Loathing got onto the ship’s hull, and Fear used the station computers first to blow up the Pegasus and then to attack the Doctor’s quarters when he took a sample from Jason’s journal for analysis. Nevertheless, enough Loathing from the original contamination has survived in the cargo bay to contaminate the survivors in Greenwich Village -- and when Easter put David in the ReGene machine on default, it assumed that the Loathing was part of him and rebuilt his DNA incorrectly. The mutated David burned himself on the rusty barricades because the rust covering the Station is a weapon created by Fear -- and Anji has come to destroy the Station and spread the rust throughout Jupiter’s atmosphere, destroying Loathing once and for all.
The Doctor reveals that he survived the third-degree burns to his body and was mistaken for Jason McCray because his DNA was in flux, as if his entire body was trying to regenerate itself; for some reason, the part of his mind that controls this process shut it down before it was complete. He admits to the shocked villagers that he’s not human, but, haunted by the memory of the young man he shot to put him out of his misery, vows that everyone here will get out alive. The Doctor repairs the ReGene unit, while Caroline finally gives in to tears after four years of trauma and admits to Robertson that she’s no longer the person she wants to be. The Doctor puts her in charge of the evacuation while he and Robertson go to the hub to break through the “energy barrier”; it is in fact the bubble of stasis fluid, and when Robertson fires an electrical pulse through the barrier, the bubble reverts to fluid state and collapses.
The Doctor fires a grappling hook up the lift shaft and drags Robertson into the Avatar chamber, where only a few moments have passed since his departure. When he arrives, however, Valetti realises that he’s older than he should be, recognises the insignia of the Professional programme on his uniform, and agrees to isolate the ship’s reactors on the Doctor’s say-so. The Professionals are alien prisoners who have been brainwashed, given false identities, and effectively been reprogrammed as cold-hearted soldiers fighting for Earth; after the burned Doctor was mistaken for Jason McCray and shot off into space, his body was found and identified as alien, and he was taken to Mars and turned into a Professional. His memories have only returned because the remnants of AuDoc, following Fitz’s instructions to join the dots, created an image of a unicorn -- the animal that the Doctor identified with in his psych profile.
The Mukabis determine that the Station is indeed inside Jupiter’s atmosphere and that there’s a four-year discrepancy between the chronometers in the hub and on the rim. Valetti is still wary of the Doctor until one of the aliens emerges from the lift shaft and attacks, having been sent by Anji to kill the Doctor before he ruins their plans. The Doctor stuns the monster with a damaged electrical cable and shuts the lift doors to keep the others out -- and then shows Valetti a familiar implant in the back of the creature’s neck. Just as he’d warned her, the implants are capable of reprogramming a human brain against its will; the “aliens” are John McCray and the 101st, and their minds have been reprogrammed by Fear. The virus needed to keep the Station intact until it was covered with the rust weapon, and to that end, it cut off the Station’s support staff from outside help and placed them in a situation where they’d have to work constantly just to survive and keep the Station intact. The 101st turned themselves into monsters using the ReGene unit in order to keep the survivors off-guard, too busy to think about what was happening to them.
Valetti accepts that the Doctor has been right all along, destroys the Mukabis’ computers and orders a full evacuation. As the systems in the hub come back online, four years out of synch with the rest of the Station, power surges and overloads cause the unstable Station to begin collapsing around the survivors. The Doctor puts on his Professional persona, contacts O’Connell and frightens the pilot into agreeing to be at a certain point in Jupiter’s atmosphere in 30 minutes or else. The Doctor then creates a gaseous mixture of Loathing from a sample of David Verger’s blood, and has Valetti launch torpedoes of the substance into Jupiter’s atmosphere to deal with the pockets of Fear that remain. He and his allies then lure the 101st into a trap and stun them using the gas; however, John McCray manages to escape, and the Doctor and Robertson go after him, refusing to leave anyone behind. Meanwhile, Anji arrives at the reactors to find Fitz waiting for her, and he reveals that, following the Doctor’s instructions, he’s already set them to overload. Anji hesitates, confused, and Fitz knocks her out and carries her to the loading tube.
The torpedoes of Loathing cause an enormous storm to build up in Jupiter’s atmosphere, pushing the Station up to a point at which O’Connell’s shuttle can safely dock with it. Once the evacuees board the shuttle, O’Connell prepares to take off, but Caroline puts a knife to his throat and refuses to let him leave until Robertson has returned. Meanwhile, the Doctor and Robertson find McCray hiding in the Avatar chamber, the last place where he felt in control of himself. The Doctor gives Robertson his grappling hook to use as a weapon, as it appears that they’ll have no choice but to drag McCray out of the chamber by force -- but then Jason arrives and tells his brother that it’s time to stop fighting, and after a moment, McCray emerges from hiding and flees back to the shuttle with them. As they board and O’Connell starts to close the ramp, the unstable Station collapses beneath them and Robertson falls out of the shuttle moments before the ramp shuts. O’Connell has no choice but to launch, and Caroline rushes down to the hold -- to find that Robertson fired the grappling hook into the hold and pulled himself back in at the last moment. With the weight of the evacuees, the shuttle doesn’t have enough fuel to reach escape velocity, but when Farside’s reactors explode, the force pushes the shuttle out of Jupiter’s atmosphere and safely out into space.
The Doctor, who remembers every moment of the last four years, returns to Mars, breaks into the Professional unit and has some words with his fellow Professionals; soon afterwards, news breaks that the Professionals have disbanded and that MacNamara has been found in a daze with no memory of the last four years. The Doctor also uses a ReGene to clear the last traces of Fear out of Anji’s system; however, the process will also erase her memory, as everything she’s done for the past four years has been filtered through Fear. Before her memories disappear entirely, she arranges for a quiet, relatively painless divorce from Michael. The Doctor visits Valetti one last time, and she confirms that, since the Avatar project was illegal, the Mukabis have no evidence to support their accusation that she’s been conspiring with alien infiltrators. Jason McCray’s mind has cleared thanks to his link with the Doctor, and he will help his brother and the 101st to recover from their mental trauma, although their bodies will never fully physically recover from the strain of having their DNA completely resequenced twice. Valetti promises to ensure that the people of Earth understand that they don’t have to turn themselves into monsters to fight threats that may not even exist. The Doctor returns to the TARDIS, where Fitz and Anji are waiting for him; there, Fitz reminds the Doctor that they need to have a talk about his past before Fitz himself forgets what happened. However, when the Doctor recalls the terrible things he did as a Professional, he decides that the past is best left alone -- and he sets the controls of the TARDIS to take him to the future, where the possibilities are endless.