Rigan, the chief of security at the Klyst Institute, checks in on the patients and experimental subjects -- especially the newest patient, the Doctor. He appears to be just as mad as all the other unfortunates in the Institute, but Rigan is paying close attention to him, unaware that it’s another of the subjects, number K-14, who is about to cause her serious trouble. Meanwhile, Mel has been left alone in her future while the Doctor attends to business, but when the TARDIS returns for her, he isn’t inside...

1957: a German immigrant named Johannes Rausch is having trouble finding work in England until a man named Louis offers his assistance. To prove his credentials before they talk business, Louis tells Rausch to go home and wait for a phone call from his daughter Carol, who is about to inform him that she’s engaged to be married. Rausch is sceptical, but Carol calls him just as Louis had predicted, and the stunned Rausch returns to the pub to find Louis waiting for him. Louis offers to use his contacts to improve Rausch’s life in small but significant ways; in exchange, he wants Rausch to promise that he will accompany Louis to a scientific institute on the day before his death. Louis is vague about exactly what will be done there, but Rausch gives in to temptation and signs the contract. Louis returns to the Institute, where Rigan prepares to set up a security detail for Rausch when he arrives; however, she first intends to investigate an odd scratching noise, almost like rats in the walls. Louis reports to the head of the Institute, Klyst, who has mapped out Rausch’s pickup point and tells Louis that he can drop by the next day...

Approximately 50 years have passed for Rausch when Louis returns, looking not a day older (though he is, in fact, exactly a day older). Louis gently reminds the shocked Rausch that he’s had 50 years to prepare for this. Rausch is an honourable man, and despite his fears he concedes that he must honour his obligations and agrees to leave without causing a scene. They are unaware that they’re being observed by Mel, who has hired a cab to drive her to this house. She tells the cabbie that she’s waiting to follow a couple of friends to a party, but he can tell that she’s lying, and she gives in and explains that she’s been told to follow Louis in order to find a missing friend of hers. Louis and Rausch emerge from the house and drive off, and the cabbie agrees to follow them, though he warns Mel that he doesn’t want to get mixed up in anything shady.

In the Institute, Klyst talks to the Doctor, trying to get through the shell of his madness to the person within -- but he’s confused and disoriented, and seems to be uncertain exactly who he is. He remembers that he used be an explorer, and even now he seeks new information and data, but it’s as if he’s unable to integrate the new information into his memories as he should. Meanwhile, Louis returns to the Institute with Rausch, and as Rigan’s guards escort the confused old man off to his room, Louis notes Rigan’s lack of sympathy for her new charge’s confusion. However, she is disgusted by the primitive species she has to mix with in this job, and doesn’t envy Louis his talent for empathising with them.

As Rausch settles in, he hears a scrabbling sound like rats in the walls, and hears someone talking to himself in the next room. He investigates and meets the Doctor, who claims to be shackled to this place, or perhaps to another person; Rausch doesn’t understand what he’s talking about, but the Doctor claims that Rausch is too limited to comprehend. But now the Doctor, too, is more limited than he should be. Klyst finds Rausch speaking with the Doctor, and claims that the Doctor suffered a tragic accident that left him like this; Klyst is trying to restore his sanity, but doesn’t hold out much hope of success. Rausch is unnerved by his surroundings, which look like a Victorian mental home, but Klyst assures him that the Institute’s equipment is modern. Rigan then rushes up to inform Klyst that the Feledrin subject, K-14, has escaped from custody, and Klyst leaves to lock down the Institute while Rigan escorts Rausch back to his room. Rausch asks why he’s been brought here today if he isn’t ill, and Rigan callously informs him that he was due to be stabbed to death tomorrow after confronting a burglar in his home. Shocked, Rausch realises that Rigan has not informed the police, and asks Rigan what will happen to the other people the burglar encounters if he isn’t captured; however, Rigan doesn’t particularly care.

Rigan returns to speak with Klyst; the Feledrin is still missing, but Rigan believes that the Doctor poses a greater threat. She has finally been able to identify him as a Gallifreyan, known terrorist with a long list of outstanding warrants on charges of sedition and even genocide, and she insists that he be detained and handed over to the proper authorities; however, Klyst insists on holding him here so she can try to cure him. Rigan is convinced that he is faking his condition in order to keep them off guard, but Klyst has made a thorough study of her patient; his condition is genuine, and he has recently regenerated.

The cabbie is bewildered by this sight, as he’s seen people walk in and out of the building’s front door before. Mel explains that when she entered the TARDIS, looking for the Doctor, she found a holographic message giving her Rausch’s address and instructions to follow Louis. Despite her unbelievable story, the cabbie finds that she somehow comes across as honest; however, while he’d like to help her, there doesn’t appear to be a way in to the impossible building. Nevertheless, Louis must have gone somewhere, and as Mel tries to work out where, the TARDIS materialises in the grounds, much to the cabbie’s shock. Mel is surprised to find that the TARDIS has followed her, apparently of its own accord; although she knows the TARDIS has a mind of its own, she wasn’t expecting the ship to act on it. Nevertheless, she enters the console room, where she sees the scanner pointed at a particular spot on the building’s wall. When she and the cabbie investigate, they discover that this part of the wall is just a holographic projection, and they are able to step through it and enter the building.

Rigan is supervising the search for the missing Feledrin, Shokhra, who is definitely no longer in K-wing and could be anywhere in the Institute. Klyst reveals that Shokhra worked in a power plant, where it was due to suffer a fatal accident; perhaps it has made for more familiar territory. Rigan sends her guards to the power core, but they are caught and overpowered by the escaped Feledrin. Meanwhile, Klyst conducts preliminary tests on Rausch, who has come to realise that Louis left out some pertinent information when they made their deal; he said that his people wanted to monitor Rausch’s brain waves as he died, but if he’s not due to die of natural causes, the scientists must intend to kill him. Klyst assures him that this is not the case, but she’s lying, and she feels guilty about it. She unburdens herself to the Doctor, who makes a good sounding board for her doubts about the project. The Doctor seems to believe that he is causing the rattling behind the walls, or perhaps that he’s been turned inside-out -- but though his comments aren’t entirely lucid, they do seem to be direct responses to Klyst’s half of the conversation. Rigan is listening in from central control, and is convinced that the Doctor is faking his condition in order to lead Klyst into sedition.

Mel and the cabbie find themselves in a garage containing some very unusual-looking vehicles indeed. Another door leads out of the garage into the interior of what looks like a Victorian nursing home, although there was no room for this vast building to fit in the hollow shell that Mel and the cabbie saw outside. The corridor is deserted, there are no electrical sockets in the walls, and they can hear voices babbling in the distance and rats scrabbling behind the walls. Mel eventually finds a room with a computer terminal, but the interface, though vaguely familiar, is like nothing she’s seen on Earth. Despite her unfamiliarity with the operating system, she manages to locate a map of the Institute, and heads for the Doctor’s cell with the bewildered cabbie tailing along behind.

Rigan removes the Doctor from his cell to question him properly, intending to use some of the Institute’s furnishings -- such as the electroshock equipment -- to get a confession out of him. The Institute was constructed like a Victorian institution because the materials don’t conduct power and aren’t susceptible to electromagnetic interference, but to Rigan, it resembles a prison, and she’s trapped inside it. The Doctor babbles to her, requesting upgrades, insisting that he never came to this place, and apparently claiming that Klyst got sense out of him because she has a more user-friendly interface. Louis then arrives to warn Rigan that the Feledrin has overpowered two of her guards, and is disgusted to find her on the verge of torturing the Doctor. Rigan remains convinced that the Doctor is faking his condition as part of a plan to destroy the Institute, but when Louis reports the incident to Klyst, Klyst insists that the Doctor is genuinely ill. Rigan is growing bored with her posting, and when someone like Rigan gets bored, others suffer. Klyst orders Louis to take the Doctor back to his cell.

As Mel and the cabbie approach the Doctor’s cell, they find the unconscious guards -- and the creatures causing the rattling in the walls swarm out into the open and surround them. Instead of attacking, however, the six creatures merge into each other, creating a single gestalt entity: Shokhra, the escaped Feledrin. He speaks in a multitude of voices (including one rather familiar one), and notes from the cabbie’s shocked reaction that he is from a world that has not made contact with alien life. Mel explains that she travels with an alien called the Doctor, who may be able to help Shokhra escape from the Institute if that’s what he’s trying to do -- and for some reason, Shokhra seems to have no trouble accepting this claim. He accompanies Mel and the cabbie to the Doctor’s cell, but they find it empty. The confused Rausch then emerges from his own room, and when he sees Shokhra, he concludes that he is dying after all and is beginning to suffer from delusions.

With seconds to go before the window gives way, the cabbie finds a cupboard containing pressurised spacesuits. Shokhra can survive exposure to space for several minutes, but Mel forces the Doctor into a suit though he also claims not to need one. Mel and the cabbie also don suits and thus survive when the window blows out. Once the airlock has depressurised, they emerge onto the surface of an asteroid. The Doctor appears calmer and more lucid out in the open, but that’s because he claims that he’s out where he belongs, amongst the stars. Mel and her allies set off in search of another airlock, keeping to the shadows to avoid attention and the heat of direct sunlight; by this point, the cabbie has decided that it’s simpler to accept the weirdness and just assume that he’s dreaming all of this.

In the main lab, Klyst sedates Rausch and engages the “grafting” process. Once it’s complete, Johannes Rausch no longer exists, and the thing in his body tries to rip off its own face. Klyst and her attendants sedate Rausch, and Klyst, upset by the results of her experiments, sabotages the security station and sets off to rescue the Doctor’s friends from Rigan. Rigan is now determined to turn the Doctor over to the authorities, thus proving her competence and winning a promotion away from this dead-end assignment. Despite Klyst’s attempts to foil her, Rigan detects the fugitives’ life-signs in M-wing, where amphibious methane-breathers are housed, and orders the guards to activate the sedation protocol. Mel and her allies are trapped in the corridors of M-wing as bulkheads slam shut and the air fills with knockout gas, but at the last moment, Klyst arrives and ushers them to safety through a hidden door. Klyst shelters the fugitives in her office, where Mel, realising that Klyst may be reasonable and open to explanations, asks how the Doctor came to be in his current condition.

Klyst explains that the Doctor arrived at the Institute shortly after Louis brought in Shokhra. While Klyst was calibrating her machines to work on a Feledrin, the Doctor emerged from the cleaning cupboard and introduced himself to the stunned Klyst, claiming that he’d stowed away in Louis’ car to get here. He’d already worked out that Louis was luring in subjects by promising to improve their lives, and Klyst confirmed that, once they arrived, she was using their bodies as hosts for complex artificial intelligences created within the Institute’s block transfer generators. The project’s aim is to create time-sensitive agents within species capable of developing time-travel technology so that the development of such technology could be monitored and controlled. The Doctor was appalled to learn that the donors’ minds were erased by the process, but Klyst insisted that they only choose people who are about to die; as far as the Web of Time is concerned, they are already dead. However, even at that point, she was having doubts about the ethics of her project; too many of the AIs were suffering from trauma when placed in humanoid bodies, and as the Doctor pointed out, failure on this front could lead to even more morally questionable methods of achieving the same goals.

Rigan then caught the Doctor speaking with Klyst and placed him under arrest, holding him in Klyst’s office. Privately, Klyst admitted to Louis that her conversation with the Doctor had her doubting the ethics of the experiments, but Louis insisted that, in this case, the ends justified the means. Left to his own devices, meanwhile, the Doctor activated the communications circuit in Klyst’s office, impersonated Rigan’s voice and tricked his guard into leaving his post. He then returned to Klyst’s lab to study her systems and try to sabotage them, and Klyst arrived too late to stop him; while trying to shut down the system, the Doctor accidentally activated it, and the circuitry discharged into his body, overwriting his own personality with one of the newly-created artificial intelligences. Klyst has kept the Doctor here ever since, in the hope that she could find some way to restore his mind, but her training tells her that this is a vain hope; even if she could remove the AI from the Doctor’s brain, nothing of his own mind is left inside.

Shokhra now explains that Louis approached him to make the Institute’s standard deal, which he accepted; however, the Doctor contacted Shokhra shortly afterwards, claiming to have an interest Louis’ activities, and Shokhra agreed to let the Doctor accompany him to the Institute on the day in question without Louis’ knowledge. Somehow, Shokhra is able to continue the Doctor’s story afterwards, even though he’d left Shokhra at that point and was acting alone. After speaking with Shokhra, the Doctor smuggled himself into the Institute by hiding in Louis’ car, and eavesdropped on a conversation between Louis, Rigan, and Klyst. He thus learned that Louis’ next target was a human named Johannes Rausch, and, with little time to lose, the Doctor rushed back to the TARDIS and programmed it to return for Mel, with a holographic message instructing her to go to Rausch’s house and follow Louis in order to find him.

While Klyst and Shokhra are telling their stories, developments are occurring elsewhere. The thing in Rausch’s body lurches back to life, rips himself free of his restraints and stands, trying to focus on the few dimensions available to him. Up and about, Rausch finds Louis and demands to be shown the way out, claiming that the barricade around the Institute will not pose a problem; Louis tries to stall him, but Rausch is prepared to use force if necessary. Louis has no choice but to lead Rausch to the entrance, where Rausch lowers the barrier and escapes to Earth. Alarms go off throughout the Institute as the barrier is lowered, and Rigan investigates to find Louis recovering from Rausch’s attack. They set off to organise a pursuit, confident that Rausch will be unable to escape from Earth without a TT capsule.

Klyst orders Rigan to pull herself together, and helps the shaken security chief take the newly-regenerated Louis to her office. Shokhra’s bodies then separate themselves from the Doctor, who reveals that he’s fully recovered; Shokhra’s gestalt mind homed in on his after their first meeting, and shared the burden when the Doctor accidentally grafted the AI into his brain. Thus, although the Doctor’s mind was distracted fighting the AI for control of his body, his memories were not overwritten. Now, however, Shokhra has taken the burden onto himself, and it’s too much for him to handle; before long, his mind will be overwritten by the alien sentience. The Doctor now reveals to Mel that Klyst, Louis, and Rigan are all Time Lords, playing god with the lesser species -- but now Klyst and Louis have their doubts about what they’re trying to achieve, and the Doctor may be able to convince them that the experiments they’ve conducted so far are proof enough that their plans won’t work.

Once Louis is settled in, Rigan turns on Klyst, blaming her incompetent management skills for the fiasco and announcing that she will now take charge of the Institute. She blames the fugitives for the loss of one of Louis’ lives, refusing to accept that the accident was entirely her fault, and announces that she intends to send the Doctor back to Gallifrey under arrest. She threatens to execute the cabbie and Mel unless Klyst agrees to use them as experimental subjects, but Louis manages to calm her down and convince her that all she needs to do is erase their memories. Before doing so, however, she intends to question them first, to find out how much the human authorities know about what’s happening here. Meanwhile, Rausch has returned to Earth, but not just because this is where his human body was born; he’s come for the Doctor’s TARDIS, which has been calling to him. Rausch tells the TARDIS that others of their kind are trapped and in pain, and the TARDIS allows him to pilot it into the Institute. There, he proceeds to the patients’ wings and releases his fellow subjects, telepathically soothing them and telling them not to worry.

A segment of Shokhra separates from the rest of the gestalt to help the Doctor and Mel study the AI generator. Mel works out that the artificial intelligences being created are TARDIS minds, which the Time Lords are trying to plan inside humanoid bodies. The Doctor confirms this and points out the experiment’s basic flaw: TARDIS minds are far too complex to fit inside the limited perceptions of a humanoid brain, even that of a Time Lord, and the newly-generated sentiences are being driven mad by sensory deprivation. Shokhra insists that the Institute be destroyed, but the Doctor refuses to sanction wanton violence, especially as the CIA would just restart the operation somewhere else. Smashing the equipment isn’t enough; they must stop the very idea of the experiments.

Rigan then takes Mel away for interrogation, but Mel refuses to let Rigan bully or provoke her. Rigan, frustrated, asks Louis to help, as he has more experience dealing with humans than she does. However, Mel understands the “good cop, bad cop” routine, and doesn’t succumb to Louis’ charm. She questions why Louis thinks he has the right to take people away from their loved ones and conduct deadly medical experiments on them, but he insists that they have a choice and would have died in any case. He concedes that he does everything he can to ensure that they agree to come with him, but claims that he doesn’t force them to make the bargain against their will. However, Mel then questions what he does if they accept the bargain but then break the contract when he comes to collect them. Realising that Louis is a good man at heart, she urges him to make Rigan see sense before it’s too late; Rigan was horrified when she accidentally shot Louis, which proves that she’s still a good person despite her bad choices. Louis may still be able to stop her before she goes too far. After a moment’s hesitation, Louis releases Mel and agrees to help her shut down the experiments.

The Doctor and the cabbie try to do what they can for Shokhra, but Rigan arrives and orders them to stand away from the AI generator. Frustrated, the Doctor demands to know the purpose of these experiments, and Klyst explains that the High Council have foreseen a time when other, less responsible species will have developed time-travel technology. These experiments are meant to plant time-sensitive agents amongst the lesser species so the Time Lords will be able to monitor their development and put a stop to it if they feel it’s going in dangerous directions. However, Klyst admits that their first attempts to work on Daleks didn’t go very well, and the Doctor wearily realises that his people are ignoring the real threats to the timelines and concentrating on weaker species that they can manipulate without risk to themselves. Louis then arrives with Mel and insists that the experiments must stop; the success rate is far too low to justify the casualty rate. Rigan refuses to listen to them, however, and when Rausch seizes control of the Institute’s systems, she takes her guards to stop him. However, Rausch and his followers now outnumber the guards, and Rausch has instituted a state of temporal grace, ensuring that the guards’ weapons don’t work. Frustrated, Rigan retreats to the control room to contact the CIA and request reinforcements.

Klyst helps the Doctor tend to Shokhra, who is still struggling to resist the sentience trying to overwrite his mind. Fortunately, unlike the other victims of Klyst’s experiments, it has not become violent; while it was inside the Doctor’s mind, it was connected to his TARDIS through their symbiotic link, and the fully-functioning TARDIS eased its fears and confusion. Unfortunately, the Doctor and Klyst have nowhere to put the sentience once they remove it from Shokhra, as it has evolved too much to fit back inside the block transfer generators, and placing it inside another living body would erase that person’s mind. However, as Shokhra struggles to communicate with them, Mel realises that he’s suggesting that they place the sentience within the Institute itself; though incapable of time travel, the Institute is still a block transfer creation like a TARDIS and is thus capable of housing the intelligence.

As the Doctor and Klyst connect the uplink helmet to the Institute’s computer network, Klyst reveals that there’s still a problem; though she has agreed to halt the experiments, a skilled technician with a mind probe could still uncover the technical data from her memories, allowing the CIA to continue their work without her. She points out that this problem could be solved if she takes a graft herself, but the Doctor refuses to let her consider committing suicide. He and Klyst then finish their work and draw the sentience out of Shokhra -- but before the Doctor can stop her, Klyst grabs the controls and downloads a sentience into her brain, overwriting her own memories and personality. Rausch arrives just in time to calm down the panicking new life form before she can damage herself, and explains that the Doctor’s TARDIS reached out to him at the moment of his “birth,” calming him down and teaching him how to live within the limitations of his new body. He is passing on this knowledge to the rest of his brethren, and now he and the sentience within Klyst can help to help the victims of the experiments.