Recent events have taken their toll on the Doctor and Chris, and the Doctor, looking for a simple, easy problem to solve, takes Chris to investigate a minor temporal irregularity in 17th century Japan. He materialises in a ruined castle where he once fought the jiki-ketsu-gaki, a type of vampire, and takes Chris to the nearby monastery where he recovered from the ordeal and found the strength to continue. He claims to be ensuring that fallout from his previous adventure is not responsible for the anomaly he has detected, but the chief monk, Kadoguchi-roshi, knows why the Doctor has really come, and the Doctor must admit the truth; he knows that his next death will be an accident, and he wants Chris to take on the role of Time’s Champion when he is gone. Roshi tells the Doctor that something has fallen from the sky near the village of Hekison, healing villagers and causing crops to grow unnaturally fast. The Doctor and Chris set off to investigate, but they have arrived in the Age of the Warring States, when the Shogunate is falling apart and rival feudal lords are vying with one another for power. Anything could tip the balance, and thus Gufuu Kocho has sent his samurai to Hekison to investigate the tales of the village god. The samurai capture the Doctor and Chris, and when the gaijin prove to know nothing, the samurai decide to kill them.

The Doctor and Chris are saved by two people armed with fireworks which startle the samurai and frighten them off. One of their rescuers is an old friend -- Joel Mintz, who still works with Admiral Isaac Summerfield in the 20th century. He helped his fellow traveller, Penelope Gate, to escape incarceration in a mental institution when she arrived in 1996 claiming to be a time traveller from the Victorian era, and when it became clear that she intended to continue exploring he asked to accompany her on her travels. The Doctor and Chris return with them to Hekison, where tension soon develops between Penelope and the Doctor. She believes that, like the men of her own time, he is being abrupt and patronising towards her simply because she’s a woman. He, however, believes that she is not all that she seems; her Analytical Engine should not be able to function without a power source capable of transporting it through Time, and indeed she and Joel appear to be stranded in Hekison. He studies the pod which fell from the sky, but is unable to determine either its origin or the source of its powers -- and the villagers, who believe it to be an avatar of the god Kannon, will not heed his warning that by keeping it here they risk attracting attention from the warlords in the vicinity, and getting themselves killed.

Terrified samurai under the banner of the warlord Umemi enter the village, fleeing from demons in the forest. The villagers’ protector, a ronin named Kame, attempts to hold them off but is struck down and killed. The Doctor and Chris are taken prisoner, and must sit by and watch as robot camera drones fly into the village, ignore the terrified samurai, and depart after locating the pod. The samurai attempt to investigate the pod but are expelled from its hut by an invisible force, and Kame then returns to life and drives them out of the village. He is unable to explain his resurrection, and the Doctor is unable to determine whether the pod is an artefact or a living being. All he knows is that two rival warlords are now aware that something powerful is present in the village, and if they do battle over it the villagers will be caught in the crossfire. Gufuu’s samurai return, but this time they invite the Doctor to speak with Gufuu. He accepts, hoping to convince the warlord to leave the pod alone, and to his surprise Joel asks to accompany him.

The Doctor leaves Chris in charge, despite Chris’ protests that he can’t handle the responsibility. Ever since he let Liz die in Turkey, Chris has been consumed with guilt and self-doubt, and he has recently been having nightmares in which he is trapped in a small confined room with no way out. What he doesn’t know is that Penelope has been having the same dreams, which she assumes represent her fear of being stifled and tied down by the patronising men of her time. The Doctor and Joel, meanwhile, are brought before Gufuu, and the Doctor tries to convince him that a war over the pod will harm the innocent without benefiting him; it is better to let Umemi expend his resources trying to capture something he cannot control. Gufuu orders the Doctor to return to Hekison and make a thorough study of the pod before he makes his decision, and declares that Joel will remain with him to ensure the Doctor’s co-operation. The Doctor has no choice but to agree, seemingly unaware that Joel, for reasons of his own, had actually requested privately to remain...

As Chris tries to convince the villagers of the risk they run in keeping the pod, a flock of alien birds, Kapteynians, arrives in the village to reclaim their property. They refuse to explain what the pod really is, however, and as Chris tries to negotiate with them, Umemi’s samurai arrive to claim the pod for their master. Before Chris can stop them the Kapteynians open fire, and in the midst of the battle, Gufuu’s samurai return with the Doctor and immediately attack their rivals. By the time the battle is over Umemi’s samurai have been defeated, the Kapteynians have fled, Kame has been killed and resurrected again -- and the village has been razed to the ground, its occupants slaughtered. The surviving villagers are taken prisoner by Gufuu’s surviving samurai, but the Doctor connects his temporal energy detector to Penelope’s time machine, providing it with a power source, and transports them all to safety in the forest.

The Doctor has Kame lead the villagers to Roshi’s monastery, while he, Chris and Penelope take a roundabout route with the pod to draw off the samurai. They manage to shake off their pursuit and pull into Toshi town to consider their next move, but there, the Doctor once again alienates Penelope with his sudden intensity when she mentions her dreams of a room with no doors. She assumes that he is refusing to explain his interest to her because she is a woman, and storms out to find the Kapteynians; she has at least accepted the Doctor’s claim that her time machine has no power source, and assumes that the Kapteynians brought her here for reasons of their own. The Doctor is then captured by a Caxtarid slave trader named Te Yene Rana, who claims that the pod is a vital part of her spaceship which her escaping Kapteynian slaves stole. He escapes from her before she can torture the location of the pod out of him, but she shoots indiscriminately after him, causing a fire which quickly spreads through town. Umemi’s samurai arrive in the midst of the chaos, and the Doctor sends Chris to safety with the pod and gives himself up to the samurai, hoping to talk sense into Umemi. Unfortunately, Te Yene Rana has already contacted Umemi, hoping to use him to get to the pod, and has promised him that the pod will give him ultimate power over his rivals. Umemi has the Doctor held prisoner, and prepares for war with Gufuu.

Penelope, trying to find the Kapteynians, is herself captured by Gufuu’s samurai and taken to the warlord -- where she learns that Joel has been teaching him how to convert a weaving loom into an automatic calculating machine. For years, Joel has worked to keep the world safe from alien invasion, but all his efforts have gone unrecognised and the world at large regards him as a sci-fi geek. He has had enough, and he joined Penelope intending to travel into the past and use his technological knowledge to change things for the better and get the recognition he deserves. Realising that Gufuu will have her killed if she does not help, Penelope convinces him to let her contact the Kapteynians so they can help her repair her time machine; in fact, she intends to use it to escape. Before she sets off, the exhausted Penelope sleeps and dreams once again of the room with no doors -- but this time the Doctor is there, and he tells her that this is not her dream, but his. For his crimes, his seventh incarnation is doomed to be imprisoned within a cell inside his own head, just as his sixth self was walled up for fear of what he would become. He assumed that Chris shared his dreams thanks to their telepathic link through the TARDIS -- but why is Penelope dreaming of the room as well?

Gufuu’s and Umemi’s samurai face off on the plains, preventing Kame and the villagers from reaching the monastery in safety. Chris arrives with the pod, and Penelope and the Kapteynians arrive as well -- but the Kapteynians are not responsible for bringing Penelope here after all, and they still refuse to explain what the pod really is. Using the Doctor’s temporal detector as a power source, Penelope programmes her time machine with an experimental configuration which the Doctor had discussed earlier, and walks into the monastery through the fourth dimension. Roshi tells her of a secret passage which the villagers can use to evacuate into the monastery -- but by the time she gets back to the forest, the battle has already started. In the heat of battle, Joel kills an enemy soldier who was attacking him, and the Kapteynian Talker attacks Te Yene Rana, allowing the Doctor to escape. He tries to help guide the villagers to safety, but the battle spills over from the plains into the forest, and the villagers are once again caught in the middle. While trying to protect a young child, the Doctor gets an arrow through the chest, and, telling Chris to get the villagers to safety, he dies -- the victim of an unpredictable, unplanned accident.

After burying the Doctor’s body, Chris takes the villagers through the tunnels into the monastery. Without the Doctor they have no-one but Chris to rely on, and Chris realises that he must put aside his doubts. He sleeps, and does not dream -- but awakens realising that the Doctor tricked him. By the time he gets back to the grave, however, the Doctor is gone, having dug himself out and wandered off with the body of the child he failed to save. Chris returns to the monastery, where he discovers that the Kapteynians do not possess a translation device; he can understand them thanks to the TARDIS, but how can Penelope? They need to know what the pod is before they can understand what is happening, but Talker still refuses to tell them. They therefore trick her into believing they are going to blow it up, and Penelope takes the opportunity to examine it -- and hears a telepathic cry for help. The pod is a cryogenic capsule containing a psychokinetic Kapteynian, whose deep-frozen brain is functioning at four thousand times its normal speed. Desperate and trapped with no way out, he has been crying out for help in every way he knows how, and his natural telekinetic abilities have been amplified by his increased mental activity in the cryogenics capsule. He drew Joel and Penelope into the past in the mistaken belief that their time machine was a passing spaceship, and has brought Kame back to life repeatedly to protect himself. Talker confesses that the only Kapteynian with the technical knowledge to open the pod without killing the prisoner is dead, and Penelope decides to use her time machine to rescue the Doctor, realising that he is the only one who can help them now.

The weary Doctor has dug himself out of his grave with the understanding that nobody deserves to be locked away in solitude for eternity -- not even his sixth self. For all his fears and attempts to disassociate himself from his past and future, he is the same person in all his incarnations, and he now acknowledges this and forgives himself his sins. He returns to the battlefield, where he finds that Umemi has been killed and that both armies have nearly wiped each other out. Gufuu, Joel and the surviving samurai are waiting for reinforcements so they can storm the monastery and seize the pod. Te Yene Rana tries to switch to the winning side, but Gufuu knows she can’t be trusted and therefore kills her. He then orders Joel to prove his loyalty to him by killing the Doctor, but Joel can’t bring himself to do so -- and is saved from his decision when Penelope arrives, having been transported here by Psychokinetic.

Penelope takes the Doctor and Joel back to the monastery, where the Doctor attempts to open the pod without killing Psychokinetic or deep-freezing everything within a mile. A samurai studying Te Yene Rana’s abandoned laser rifle accidentally blows a hole in the monastery wall, enabling Gufuu’s men to enter -- but the Doctor manages to open the pod first. Once he is free of the pod, Psychokinetic’s power returns to its normal, relatively weak state, and the pod becomes useless as a weapon. Gufuu, however, knows that he will lose the respect of his samurai if he takes out his frustration on those who have thwarted him, and therefore simply turns and walks away.

The Kapteynians decide to remain with the villagers of Hekison and help them to rebuild their home. Psychokinetic discovers that his time in the pod has indeed affected his powers, but only time will tell how strong he has become. The Doctor considers leaving Joel in the monastery to teach him a lesson, but cannot bring himself to leave Joel trapped somewhere with no way out, and decides that Joel has had enough sense shocked into him. He takes Penelope back to her own time, where she will continue to fight for her independence although she knows that she will never achieve the recognition she deserves. The Doctor and Chris are both at peace now, having forgiven themselves their failures. The room with no doors will not be waiting for either of them.