The commanding officer General Smythe, who is based at a nearby chateau, is rather enigmatic and secretive. He has a secret communications device in his chambers through which he requests a further 5000 specimens for his section, and also seems to be able to disappear for short periods from his private quarters. His subordinate, Captain Ransome, questions him on this behaviour and Smythe responds by donning a pair of glasses and exerting some sort of mental control over Ransome to make him forget what he has seen. When the Doctor and his companions are brought before him, Smythe decides to hold a court martial, producing a distorted report on their activities since arriving in the trenches. The Doctor tries in vain to challenge this version of events, calling Carstairs and Lady Buckingham to offer evidence in his defence, but Smythe has made up his mind. When the military judges retire to consider their verdict, Smythe uses his hypnotic abilities to persuade Barrington and Ransom to agree that the prisoners should be punished; Jamie is to reassigned to his “regiment” for further court martial; Zoe will be incarcerated for ten years as a spy; and the Doctor himself will be shot. The trio are separated as they await their fate.
During the night Zoe sneaks away from Lady Jennifer, under whose protection she has been placed, and starts to investigate the chateau. She manages to free the Doctor, but before they can escape Ransome finds them and announces the execution is imminent. With Zoe made to watch, the Doctor is attached to a firing post, and the firing squad prepare to fire.
The execution squad is interrupted by a sniper, allowing Zoe to free the Doctor and they flee to the military prison where Jamie is being held. He has meanwhile found himself in a cell with a redcoat apparently from the Battle of Culloden (although he gives the year as 1745 and not 1746), who claims to remember little after being abducted from the scene of the battle. Overcoming mutual enmity, they eventually stage a mock fight as a distracting ruse which enables an escape bid. The Doctor has meanwhile gained entry to the prison by posing as an Examiner from the War Office, totally confounding its commandant, Gorton. The escape attempt is reported as is the death of one of the escapees, but it is not Jamie and he is soon brought to Gorton’s office for interrogation by the “Examiner”. The Scot plays along but after a while Gorton becomes suspicious and has to be knocked out to protect the ruse. The reunited trio make to leave but soon find themselves once more prisoners of Captain Ransome.
Back in the Chateau, Smythe’s mysterious behaviour has continued and he departs for a military conference in a cupboard-like box which has materialized in his quarters. It departs in the manner of a TARDIS with Smythe inside. Ransome has witnessed this, but once more Smythe’s hypnotic powers erase the event from his memory. Elsewhere in the building, Carstairs and Lady Jennifer talk more freely, mentioning a strange mist they have both encountered. They all voice concerns about the behaviour of Smythe at the court martial. Ransome returns with news of the recapture of the prisoners, but by this time Carstairs has become so concerned at the situation that he and Lady Jennifer decide to help the three prisoners. She distracts Ransome while Carstairs sets the trio free. Jamie tells the others of the redcoat, while Zoe now reports on the strange apparatus in Smythe’s office, prompting them all to decide to take a closer look. With Ransome out of the way the Doctor and his friends investigate Smythe’s office and see the communications unit – though curiously neither Carstairs or Lady Jennifer can see it initially, evidently their minds being clouded. The Doctor realizes the unit is active and disables it, though not before Smythe and a technician at the other end have observed their interference.
The Doctor and his party now make to leave in the ambulance, once more evading the hapless Ransome by Carstairs’ quick thinking that he is taking the prisoners for further interview with Smythe in another location. When Smythe returns, he is furious with the Captain for allowing the prisoners to escape and immediately orders surveillance of the departing vehicle. It is eventually found heading eastwards in sector four. Smythe appals Carstairs by ordering that British troops fire on an ambulance with two women inside. To avoid the shelling, the fugitives drive into a strange mist which soon engulfs them and makes Carstairs and Lady Jennifer very nervous. The Doctor takes over at the wheel and drives on into a valley where they all disembark. They are there greeted by a very strange sight indeed – a phalanx of Roman soldiers is advancing on them with weapons drawn.
Fortunately the ambulance starts again in time and the party drive away, leaving the Romans bewildered. In the ambulance, the Doctor deduces they have passed through some sort of force-field barrier which is keeping time zones apart, and speculates there may be many such zones on the planet. He decides to try and get a map of the area but the only place he can think of to locate one is at Smythe’s office back in the chateau. Carstairs resumes the “prisoners and escort” routine to get them all back into the Chateau, where Ransome challenges them but is overpowered and tied up. The Doctor searches Smythe’s quarters and there uses explosives to blow open the General’s safe. This alerts a soldier to some wrongdoing, but Carstairs overpowers him. The Doctor is now able to retrieve a map, showing a series of triangles all marked with dates and names of wars in the history of the Earth. With the map in their possession, the five travelers escape in the ambulance once more – this time to cross over into German lines and be captured German soldiers.
They are all taken to the German military HQ where the Doctor is interrogated by the impressionable Lieutenant Lucke. The Doctor tells him the truth about his travels, and illustrates his technological power by using the sonic screwdriver. However, just as the Doctor is about to make a breakthrough the commanding officer, Captain von Weich, arrives. The Captain takes Lucke to one side and, donning a monacle, exerts the same sort of mental control of his soldier that General Smythe did with his men. Von Weich stalks away to report the capture of the fugitives via a communications unit, and reports they claim to be time travelers. Lucke returns to the prisoners and the Doctor succeeds in breaking the mental conditioning and soon gets hold of the Lieutenant’s weapon. He uses this to get the Lieutenant to take them back to the ambulance and, free once more, the Doctor and his friends decide to head toward a mysterious black triangle marked on the centre of the map.
This zone is indeed Central Control and is populated by technicians in neutral futuristic clothes and strange glasses. Smythe is there too and welcomes the arrival of his superior, the War Chief, who brings greetings from his own superior, the War Lord. News arrives from von Weich that the prisoner have escaped again and the War Chief is especially concerned that the fugitives claim to be time travelers. It soon becomes apparent that they are involved in some sort of war game using models to plot real conflict between the rival armies.
The ambulance has meanwhile reached the American Civil War zone. They are soon besieged by Confederate troops and Carstairs is separated from the others and taken as a prisoner to Central Control. The ambulance drives on until it runs out of fuel. The Doctor, Jamie, Zoe, and Lady Jennifer take refuge in a barn and try to get some rest. They are hidden, however, when one of the travel units materializes in the barn and a stream of Confederate soldiers pour out, heading outward to battle. The Doctor and Zoe examine the capsule but while they are inside the door slides shut and the machine dematerializes.
The Doctor and Zoe soon arrive in a docking bay for the TARDIS-type vehicles located in Central Control. They soon find some German soldiers for the First World War zone and then a Roman legion, all in deep hypnosis. The pair adopt the eye glasses of the alien beings managing the war zones and they use this disguise to explore the Central Control area. It is a vast building and they soon find themselves in a lecture hall for a presentation, where they have their fear that the war zones are on an alien planet confirmed.
Jamie and Lady Jennifer have meanwhile become embroiled in a battle between Union and Confederate soldiers which the latter forces win. However, the head of the Confederate forces is Von Weich, now wearing the appropriate uniform, and he denounces the pair as spies and has them restrained. This capture is reported to the War Chief, who instructs that they be held until they can be reprocessed. The War Chief has been in dialogue with the Chief Scientist, a nervous man preoccupied with improving the mental conditioning process to eliminate the 5% failure rate. Back in the barn Jamie and Lady Jennifer are freed by a union soldier named Harper and escape but all three are soon recaptured. It seems Harper is one of those on whom the mental processing has failed, and is also part of a broader resistance movement. A little later a squad of resistance soldiers bursts in upon the barn, seizing control and restraining von Weich.
The Doctor and Zoe witness an experiment in mental reconditioning with Carstairs as the subject. The Chief Scientist explains to his audience that technology improvements will enable even the most resistant specimens to be reconditioned. Carstairs is reconditioned successfully and immediately denounces the Doctor and Zoe as German spies. Based on this, the Scientist incorrectly infers that the conditioning hasn’t been successful and the Lieutenant is restrained and taken away. The Doctor now examines the apparatus and realizes it can be used to de-process as well as condition the human subjects. The War Chief visits the presentation and clearly recognizes the Doctor amongst the crowd, prompting the Doctor and Zoe to run for freedom. She gets separated from the Doctor but soon runs into Carstairs – who draws his revolver to shoot her.
The Chief Scientist interrupts the situation and ensures Carstairs is disarmed, still believing him to be disturbed, and then imprisoned once more. She is interrogated by the Security Chief, another of the alien leaders, who discovers her history using a futuristic lie detector. When the War Chief calls in on the interrogation, it is clear that he and the Security Chief are not easy bedfellows.
Meanwhile the Doctor finds the Chief Scientist and persuades him he is actually a devoted student, offering to assist with his work on the mental conditioning process. He persuades the Scientist to de-process the dazed Carstairs and once this is done the Doctor and the Lieutenant overpower the Scientist.
In the American barn the resistance fighters are squabbling amongst themselves, unclear of the origin of the situation. The only thing that calms the situation is the arrival of their leader, Russell, a British Boer War soldier, who asserts his authority. Von Weich uses the confusion to try and send a message to Central Control, but succeeds only in demonstrating to the resistance fighters that there is a hidden communications device nearby. Von Weich then manages to activate the emergency alarm on the apparatus.
Back in Central Control, this is relayed to the War Chief and the Security Chief, and they leave Zoe while they go to investigate. This enables the Doctor and Carstairs to rescue Zoe, while also being able to scan through the files of known resistance fighters and those on whom processing failed, alerting them to the existence and extent of this movement. However, it is also clear that not all the possible resistance are organized into a single force. They then head to the security centre and observe the Security Chief decide to respond to the emergency in the American Civil War Zone by sending a squad of troops to investigate in one of the travel machines. The troops are sent to the barn where they emerge and open fire, killing Harper, but Russell and his troops fight back and overpower the attacking troops. Russell now decides to take the fight to Central Control and outlines plans to use the travel machine to take a troop of resistance fighters to attack them. Jamie reluctantly agrees to accompany them, while Lady Jennifer is sent to the rebel HQ to help with the wounded resistance fighters, and Von Weich is left under guard in the barn.
Meanwhile the enmity between the Security Chief and the War Chief is mounting, made worse when they realize Zoe has escaped, Carstairs has disappeared, and the Chief Scientist has been overpowered. It also seems the War Chief is not of the same species as the other aliens controlling the war games and the Security Chief, realizing the fugitive pair have a knowledge of time travel and are thus probably somehow related to his rival the War Chief. The War Chief himself happens to be at the security center when news of the approaching traveling ship reaches them. He assembles a patrol of guards outside the docking station and when Jamie, Russell and the other resistance
The bodies are removed and taken to the Chief Scientist for reprocessing, while the Doctor and Zoe watch on from a secret hideout. Jamie is identified as having never been processed and is taken away for further examination by the Security Chief while the reprocessing effort begins in the laboratory. The Scientist is stunned when the Doctor appears at his side offering to help with this process, but again it is a ruse to overpower him. He revives Russell and the others, explaining his friendship with Jamie, and the band of rebels now plan to escape the control center with the Doctor and Zoe. The Doctor realizes Zoe can be of immense use having memorized the faces of each of the resistance leaders from the various war zones. It is decided to try and pull together the disparate resistance fighters into a single fighting force. The next task is to rescue Jamie from the security center and, this accomplished, they all make it to the docking station. The Doctor sends Zoe, Russell and the resistance fighters back to the war zones in a travel machine to pull together the rebel army while he, Jamie and Carstairs stay in Central Control to try and get hold of the processing equipment. When Russell’s party returns to the barn they realize Von Weich is bidding for freedom, having reconditioned his guard, Private Moor. However, they arrive just in time and Moor is able to resist once more, ending up shooting Von Weich dead.
The Security Chief is becoming obsessed with thoughts of a conspiracy between the Doctor and the War Chief. This lack of attention enables the Doctor to get back to the processing room where he steals the processing equipment. He and his friends return to the docking bay and enter one of the TARDIS-like vessels. However, the War Chief has become alert to their plans and so traps the machine and begins to manipulate and shrink its internal dimensions from outside. Inside the craft the Doctor, Jamie and Carstairs have seconds to live.
The Doctor emerges under a flag of truce, but this is but another ruse to re-enable the dimensions of the craft, which is then used to spirit the three friends away. Even more impressively, he has seized the correct circuits to allow the vessel to be independently piloted between war zones. He pilots it to the Roman zone, planning to travel on foot then to the 1917 zone where he has agreed to meet Zoe.
Back in Central Control the War Lord, leader of the aliens, has arrived to assume personal control of the situation. He is furious when he learns the extent of the Doctor’s havoc from the other war planners. They are tracking the missing vessel, named a SIDRAT, and follow it remotely to the Roman Zone. The Security Chief then tries to denounce the War Chief to the War Lord, accusing him of conspiring with the Doctor, but he dismisses this concern as unfounded.
The Doctor, Jamie and Carstairs have now reached the 1917 zone on foot, but their progress is being tracked by General Smythe, who arranges a machine gun reception for them. Fortunately Zoe and her team are able to overpower the machine gun nest but this does not prevent her three allies being taken prisoner by a patrol of British soldiers. The Doctor, Jamie and Carstairs are taken back to the chateau, where Smythe orders the Doctor’s immediate execution while the other two are assigned for reprocessing. When he reports this to Central Control, he is reprimanded for not taking all three alive and not recovering the reprocessing machine. He heads off to stop the execution, but others have the same intention. A large army of resistance fighters under Russell attacks the chateau and Smythe is just able to communicate the dire situation to Central Control before he is shot. The Doctor and his friends are now in control of the chateau, but a short while later a large force of conditioned soldiers is sent against the building, British from one side and Germans from the other. The Doctor responds by reprogramming some of the machinery in Smythe’s office, allowing a war zone with its mists to be drawn immediately around the chateau. This protects them all from attack. In Central Control, the War Lord responds to this blow by taking personal control of the entire operation.
The Doctor now uses the de-processing equipment on some captured humans and is relieved that it works. Moments later another SIDRAT arrives and a squad of alien soldiers stages a swift reprisal attack, seizing the Doctor and the processing equipment.
The Doctor is taken to central control and is interrogated by the Security Chief using the truth device. He charges that the Doctor and War Chief are both of the same race, the Time Lords, and that somehow the War Chief is planning to betray the project to his own people. The Doctor refuses to co-operate and is tortured for information until the War Chief arrives and confirms he and the Doctor are indeed both Time Lords. The War Chief then has the Doctor transferred to his own custody so that the two of them can talk, while the Security Chief fumes. The War Chief and the Doctor now talk frankly of the Doctor’s having stolen a TARDIS and absconded from his homeworld. The purpose of the war games is also revealed: the humans will be whittled down until only the strongest survive and these soldiers will then be used as an army to conquer the galaxy. The War Chief sees conquest as a means of achieving a greater peace and asks the Doctor to help him in this scheme. He of course refuses, condemning the War Chief for sharing Time Lord technology with the aliens and helping them to build the SIDRATs. The War Lord too offers the Doctor a partnership at the apex of their galactic conquest, but it is also clear the War Chief wants the Doctor to work with him alone in toppling the War Lord once the conquest is complete.
Back in the Chateau, the rebels focus on trying to assemble their resistance army using Zoe’s skill at remembering the faces identified as unconditionable. Later that night, a squad of Mexican bandits invades the Chateau and its leader, Arturo Villar, is slowly persuaded to add his force to the collective army of resistance. A council of war is held at the Chateau, with a Russian soldier named Ivan Petrov acting as the broker who finally persuades Villar to throw his troops in to the combined force. They all now work out a plan to seize a SIDRAT and fill it with a rebel army that can then be used to attack Central Control. Meanwhile small groups of resistance destroy the alien communication devices, sending the war masterminds into panic at Central Control. The rebels converge on the American Civil War zone and are waiting for a SIDRAT when the Doctor appears on the communicator, telling them he has taken control of the alien transportation system and sends a SIDRAT for them. Villar, Russell, Carstairs, Jamie, and Zoe climb aboard and the transport craft soon takes them to Central Control, where the Doctor is waiting for them. However, he is with the War Chief and the Security Chief and a squad of troops that take them all prisoner. The Doctor has sold them out to the enemy.
The prisoners are taken for processing and the War Chief and the Doctor are left alone. It seems the SIDRATs that the War Chief has built have but a limited life-span and he now wants the Doctor to help him by giving him his TARDIS. The Doctor now offers to improve the mental processing machines, and will start by reprocessing the rebel leaders. He goes to the processing room and is there confronted by a furious Villar and Russell, and the Security Chief withdraws the guards so the Doctor is left alone with the mob he has betrayed. The Doctor explains he only helped the aliens because the Security Chief threatened to wipe them all out using a neutron bomb but Villar cannot be persuaded he is an ally and attacks him. Indeed, only the timing of the War Chief’s arrival saves the Doctor’s life. The Doctor starts to “process” the prisoners – in fact doing nothing – and this ruse works well until Villar doesn’t play along and attacks the Doctor again. The Doctor’s friends now overpower the guards in the room.
Meanwhile the Security Chief reveals he has been taping the conversations between the two Time Lords and now knows the War Chief is plotting against them. He has the War Chief exposed to the War Lord and arrested. However, en route to the prison the escort is ambushed by the rebels and the War Chief is freed. They all find arms and now stage a major attack on the war planning room. The War Chief exacts his revenge, shooting dead the Security Chief during the general melee. He then reveals the SIDRATs are perishing at a rapid rate, making it impossible to get all the fighters home to Earth. The Doctor decides to stop the games nevertheless and the War Chief broadcasts to all zones telling them the war is over.
The Doctor knows the thousands of soldiers on the planet must be returned to Earth and that he cannot do it alone. Despite the warnings of the War Chief, he decides to contact the Time Lords and sends a mental appeal to them to assist. The War Chief slips away to the SIDRAT docking bay where his plan to flee ends when the War Lord appears and has his soldiers shoot dead his former ally. Moments later Villar and his troops reach the docking bay, killing more guards and taking the War Lord prisoner. The Doctor now tries to slip away, heading back to the 1917 zone with Carstairs, Jamie and Zoe in order to retrieve the TARDIS. It becomes apparent the Time Lords have arrived when Carstairs just disappears, sent back to his own time zone and planet, and a strange sound can be heard. The Doctor, Zoe and Jamie try to run to the TARDIS but their movements are slowed down and they fail to escape before the Time Lords can capture them.
The Time Lords manipulate the TARDIS containing the Doctor, Jamie and Zoe and bring it back to their planet, where the Doctor must answer for his crimes in stealing his TARDIS and fleeing his homeworld to travel the universe in contravention of Time Lord law. The trio emerge and are taken to a court chamber where three imperious Time Lords sit in judgement over the War Lord, whose trial has begun. He is charged with crimes against the humans he captured and against the galaxy for his war mongering. The Doctor confirms the case against him, denying any suggestion he too was involved in planning the games. The trial is interrupted, however, when a group of the War Lord’s personal guard break in to the chamber. The criminal now wishes to use the Doctor’s TARDIS to escape to freedom and takes the Doctor, Jamie and Zoe hostage back to the craft, threatening them if they do not co-operate with his plans. However, the Doctor and his friends evade their captors, allowing the Time Lords to assert control again. The Time Lords exact the ultimate punishment: the War Lord and his guards are dematerialized from all history as if they never existed, while their home planet is trapped behind a force-field and cut out from the rest of the galaxy.
The Time Lords now turn to the Doctor. He is formally charged with breaking the laws of time and interfering in the histories of other planets. His defense is the need to interfere sometimes to fight evil, citing the Daleks and Cybermen amongst the foes to be combated. While awaiting the verdict, the Doctor, Jamie and Zoe stage an escape attempt. The Time Lords stop them and then effect a tearful departure, returning Zoe and Jamie to their own original time zones with no memories of their time with the Doctor save for their first adventure with him. He himself is taken back to the court room and shown images of his friends being returned safely to the Wheel and Culloden respectively. The Time Lords then announce that the Doctor has convinced them that there is evil to be fought and that his own interest in planet Earth, itself a magnet for alien invasion, makes it ideal as a planet of exile for him. He will be exiled there in the twentieth century, his memory wiped of the ability to control the TARDIS, and his appearance will be changed as well. When the Doctor rejects all the facial images presented to him as alternatives, the choice is taken out of his hands. The Doctor protests in vain as his faceless body spirals into a dark void…