Back in 1913, the Doctor saved the people of Guernsey from a terrible evil, but he failed to save the life of a little girl named Celia Doras. Now, in 1941, Guernsey has been occupied by the Nazis, and the Doctor, knowing that something is about to go wrong with history, asks Ma Doras to let Benny pose as Celia in order to investigate. Over the next few months, Benny is exposed to the dispiriting and ubiquitous air of oppression under Nazi rule, and is nearly caught by a Nazi patrol when she breaks curfew to scout out a beach where the Doctor has told her something is about to happen. In order to get to the beach safely, she leads on an impressionable young German private named Gerhard who’s staying at the Doras boarding house, and convinces him to go for a walk on the beach. Just before midnight, something which seems too dark and silent to be a plane explodes in the air over the beach, and while Gerhard is occupied helping the patrols to investigate, Benny manages to steal a fragment of the wreckage and take it back to the boarding house. That night, the Doctor returns, bringing milk and claiming to have come in answer to a note which Benny doesn’t remember leaving for him. When he studies the fragment, he confirms that, although neither alien nor anachronistic, it is nevertheless evidence of something which has the potential to change the outcome of the Second World War.

Benny leads the Doctor back to the beach, where he asks her to create a distraction while he examines the rest of the wreckage. While trying to lure the German patrols away from the Doctor, however, Benny is spotted and recognised by Gerhard, and she has no choice but to shoot and kill him before he can identify her and bring retribution down upon the Doras family. The Doctor sees enough of the wreckage to confirm his suspicions, but before he can depart he is captured by Standartenführer Joachim Wolff. Wolff senses his strange prisoner’s keen intelligence, and decides to send him to the French village of Granville for interrogation by Oskar Steinmann. Benny returns to the Doras home and waits for the Doctor to return, but it becomes obvious that he isn’t going to show up again. When Wolff orders the execution of six innocent villagers in retaliation for Gerhard’s death, Benny heads for the docks, unable to face spending any more time under the Nazi regime and intending to return to mainland Britain. Wolff captures her, however, and before he can identify her as Celia Doras, she gives her real name and surrenders.

Roz and Chris have infiltrated the SID with forged papers identifying them as, respectively, South African and Canadian secret agents. Admiral Kendrick assigns Chris to infiltrate enemy territory and locate the German scientist Emil Hartung, who has been spotted both on Guernsey and at Granville and who is apparently at work on a superweapon which could help the Nazis win the war. Since Hartung’s grandmother was Jewish and he has expressed dissatisfaction with the Nazi party in the past, Kendrick hopes that Chris can convince him to defect -- but if necessary, he must be killed. Meanwhile, Roz is put to work on bomb pattern analysis with Lieutenant George Reed, who is impressed by her intelligence and world-weary demeanour. He later admits that he has been fascinated with her people ever since seeing a photograph of a Xhosa maiden in a geographical magazine as a child. Despite herself, Roz is also attracted to his steadfastness and good intentions.

The Doctor is expecting to be tortured and interrogated, and is thus more than a little surprised when Steinmann instead plays chess with him and tries to charm him into working for the Nazis. The Doctor learns that Hartung has been working at a nearby base, and thus willingly signs a document pledging allegiance to the Nazi party in order to get closer to Hartung and confirm whether he’s built what the Doctor fears he has. Meanwhile, Chris gets past the shore defenses into occupied France, and shelters near Granville with a farmer named Gerard and his seductive daughter Monique. Gerard shows Chris a fence which appears to cross the middle of nowhere, and reveals that it surrounds a secret airbase; the landing strip is painted green to blend in with the grass, and the guard posts are made of concrete shaped to resemble trees. The base is thus invisible from the air, and some German soldiers have been court-martialled simply for admitting that it exists. Chris spots the Doctor in the back of a car entering the airbase, concludes that he’s been captured, and determines to rescue him.

Wolff masterminds the breaking of the “Tomato” espionage network, and the last message to get to Britain contains the words “hoogin” and “mooning”, which nobody understands. Meanwhile, Kendrick reassigns Roz and Reed to capture a man who has been photographed in the vicinity of SID HQ several times, and who is believed to be the notorious German spymaster Doctor von Wer. Roz recognises the man as the Doctor and thus, despite Reed’s objections, she continues to work on the bombing analysis. Eventually, fed up with the chaotic and unreliable monitoring systems of 1941, she uses the TARDIS computers to analyse the records, and determines that on one particular night, fewer planes were spotted in the sky but more bombs were dropped on London. This seems to indicate that the mysterious new weapon is a superbomber capable of delivering an incredible payload of bombs. Kendrick takes Roz’s report to the War Cabinet, who decide that Hartung must be stopped at all costs and order the RAF to bomb Granville -- a primarily civilian French village.

Benny is deprived of sleep for two days and then systematically tortured by Wolff, who keeps Nurse Kitzel nearby to ensure that Benny suffers no permanent damage and can still answer questions. Steinmann arrives to send Wolff on a new mission and takes over interrogating Benny, who in her delirium and desperation has admitted that she is an archaeologist from the future. Steinmann doesn’t believe her -- not because he disbelieves the possibility of time travel, but because he believes without doubt that Germany is destined to win the war. Since Benny is not a Nazi, she cannot be from the future. Steinmann returns to Granville while Wolff goes to London to deliver an ultimatum to the British. Benny, still delirious, recalls the death of her mother at the hands of monsters obsessed with genetic purity who exterminated all that was unlike them, and in her desperation she manages to overpower Nurse Kitzel. She forces Kitzel to take her to the morgue, where she finds two bodies -- one Gerhard’s, and the other burned beyond recognition but identified with a nametag. Benny disguises herself in Kitzel’s uniform, locks Kitzel in a drawer in the morgue -- possibly condemning her to death from suffocation -- and manages to get to the docks and convince a fisherman to take her to the British mainland.

Chris kills a German soldier for his uniform and breaks into the airbase to rescue the Doctor, who is appalled when Chris happily guns down the pursuing Nazis as if it’s all part of a game. They escape from the base and return to Gerard’s farm, where they find heavy vehicle tracks in the yard, the smell of cordite in the air, and no sign of Gerard or Monique. They return to Granville, but just as they arrive, the RAF begin to strafe the town; although the British forces manage to destroy the visible German airbase, the hidden base remains untouched, and several hundred French civilians are killed.

Roz and Reed discuss past German operations and obsessions, including their re-use of old tricks which have already been discovered, and their use of Norse legends for code words; for example, using the name of the one-eyed god “Wotan” to represent a single-beam radar guidance system. This train of thought leads them to decipher the last message from the Tomato entwork -- not “hoogin” and “mooning”, but Hugin and Munin, Wotan’s two raven messengers. Whatever Hartung has built, there are two of them. A known German spy is then spotted meeting someone at Paddington Station, and Roz and Reed are sent to detain him. The man in question, Wolff, attempts to escape, as he has a message to deliver to the British government and knows that the police won’t pass him on. Roz corners him, but, overconfident that he can beat a black woman, Wolff challenges her to take her best shot; unaware that this era doesn’t have tissue regeneration capabilities, she pokes his eye out with her finger. Wolff is brought before Kendrick for interrogation, and delivers an ultimatum; unless the British agree to cease hostilities and ally themselves with the German Reich instead, the Germans will use Hartung’s new weapon to destroy a city on the south coast of England.

The Doctor and Chris are reunited with Steinmann in the ruins of Granville. Chris is shocked when he sees the Doctor carrying on a civilised conversation with a torturer and war criminal, but the Doctor has always tried to show mercy, even to monsters. Steinmann takes them to the hangar where “Munin” is kept, and Chris, expecting to learn that Hartung has retro-engineered alien technology from a crashed UFO, is rather disappointed to find that the secret weapon is in fact simply a primitive stealth bomber. The Doctor points out that it’s still capable of evading the primitive British radar of 1941, and thus could change the course of the war. When Steinmann tells them how long it took them to build the prototypes from Hartung’s designs, however, Chris realises that Hartung must have started work on his radar-invisible plane before the British had even begun to develop their radar system, and concludes that he must have been acting on the advice of a renegade time traveller.

Steinmann now admits that the second prototype, Hugin, exploded on a test run over Guernsey -- this is the explosion which Benny witnessed. The Doctor has been brought here to explain why this happened. When he is unable to do so, Steinmann tries to shoot him, but the Doctor has already removed the bullets from his gun and Chris is able to overpower both Steinmann and the two pilots who were about to use Munin to destroy Southampton. The Doctor and Chris steal Munin and attempt to fly it back to Britain; on the way, the Doctor deactivates the test signal which the Germans were using to trace the plane during test flights, but Chris then accidentally flies straight through a squadron of Spitfires which were unable to detect him. The British planes collide in mid-air while trying to avoid him, and most of the squadron is destroyed. Word of the incident gets back to Kendrick, and the SID finally determines the true nature of Hartung’s weapon. The War Cabinet decides that in order to destroy the radar-invisible plane before Wolff’s deadline expires, they will have to bomb the airstrip on Guernsey -- even though this means that they will be bombing their own civilians. Meanwhile, as Steinmann tries to organise the pursuit of Munin, he receives papers recovered from the crash site in Guernsey -- and amongst them he finds Benny’s diary and her notes on the outcome of World War Two.

Benny stops off at Allen Road, where she leaves the Doctor a note asking for rescue and telling him to bring milk. She manages to get back to London and the TARDIS before collapsing, and Roz finds her lying outside the TARDIS and gets her to the medical bay for treatment. The TARDIS then detects the approach of the Nazi stealth bomber, and Roz leaves to warn Reed as the TARDIS dematerialises by itself, apparently trying to get out of the danger zone. Meanwhile, the Doctor realises that Hugin blew up by itself due to a design flaw which causes the reserve fuel tank to overheat. Chris dumps all of the fuel in the main tank into the reserve tank, thus ensuring that there isn’t enough oxygen in the tank to start a fire, and manages to put down in St James’ Park before the fuel runs out. Benny and the TARDIS are waiting for them, but Kendrick and his men then arrive and arrest the Doctor, still believing him to be a German spy.

Benny and Roz help the Doctor to get out of jail, but Benny is still furious with the Doctor, who claims that he had no idea she was in such great danger. One day he’ll be too late, and one of his companions will be killed. When Benny tells him that she found Hartung’s charred body in the morgue on Guernsey -- he was the test pilot on Hugin’s explosive final flight -- she realises from his reaction that he already knew Hartung. He admits that he and Mel once materialised in Cairo in 1936, where they met Hartung and engaged in an innocent conversation which included a discussion of the hunting patterns of owls and bats. Many years later, he found Hartung’s diary in a vault in the Soviet Union, and realised that it was this conversation which inspired Hartung to draw the connections which led to his near-development of the stealth bomber. All this time, the Doctor has been correcting his own mistake.

Roz blows up Munin to prevent the British from studying it, and tells Reed the truth about herself; she must leave, but Reed chooses to remain and continue fighting his war. The Doctor confronts Wolff in prison, and although he never tells anyone what passed between them, Wolff ends up dead, possibly having committed suicide. As the Doctor and his companions leave 1941, the Doctor recalls Mel’s horrified reaction upon learning that the nice man she’d been flirting with was a member of the Nazi party, and the Doctor’s own realisation that he was going to have to get rid of her in order to fulfill his responsibilities. History is back on track, and over the next several months, Oskar Steinmann is forced to watch in despair as his warnings are ignored and all unfolds as Benny’s diaries described. The disastrous attempt to invade Russia leads inexorably to the defeat of the Nazi party, the end of the Thousand Year Reich, and the utter failure of Fascism -- and Steinmann lives for the rest of his life with the crushing knowledge that he had fought on the wrong side.