The TARDIS seems determined to materialize on Earth, and the Doctor does so in order to investigate and conduct repairs if necessary. He, Sam and Fitz emerge to explore, and Sam goes off on her own, still trying to come to terms with the liaison between Fitz and her other self. By the time they realize they’ve arrived in Europe during World War Two, the bridge on which the TARDIS has materialized has been bombed, dropping the TARDIS into the river and cutting Sam off from the Doctor and Fitz. While Sam seeks help in the nearby village, the Doctor and Fitz head down the river to find another bridge; instead, they find a group of German fifth columnists under attack from Americans, and while trying to get away Fitz falls into the river and is swept downstream. The Doctor is confronted by a wounded American soldier, Wiesniewski, who collapses after mumbling something about “Leshy” -- legendary wood spirits from Polish folklore. Realizing that there’snothing he can do right now to help Sam or Fitz, the Doctor takes Wiesniewski back to Bastogne for medical care.
Sam meets American Sergeant Jeff Kovacs and claims to be a British nurse; strangely, he accepts her story at face value even though she is unable to prove it. Unwilling to risk his men protecting her, he sends her back to Bucholz Station with another squad, but their column is attacked and captured by Germans at the Baugnez crossroads. Sam finds herself unable to shoot a German soldier even to defend herself, and thus she and the neighbouring soldiers are taken prisoner. The Germans, blaming the Americans for bombing German civilians, take revenge by slaughtering their prisoners with machine-gun fire and shooting each survivor individually. Sam is shot in the chest and dies. The only survivor, an American soldier named Dan Bearclaw, later tries to see whether Sam is all right, only to see lights moving about her body -- which then vanishes into thin air.
Fitz emerges from the river near a town which has been reoccupied by the Germans, and disguises himself in a dead German’s uniform, hoping to blend in until an opportunity to escape arises. Time seems to slow down for a moment, and shortly afterwards a group of armoured cars with strange antennae arrive in town, commanded by Sturmbannfuhrer Leitz. Fitz, trying to find out what Leitz knows, drops loaded comments about temporal anomalies and relativistic effects, and the curious Leitz decides to have Fitz assigned to his squad. Fitz learns that a “special” prisoner is being held in a nearby tent, made of a fabric woven through with copper and steel, and finds that he is unable to focus properly on the prisoner in the cage within. The company is attacked by strange chitinous creatures which the soldiers are able to focus upon properly, and Fitz takes advantage of the confusion to release the prisoner and escape into the woods with him. Once there, the prisoner -- who appears almost like a beautiful red-haired man, or perhaps like a glowing golden figure -- offers to take Fitz into his world, but when Fitz refuses, the creature vanishes, leaving Fitz alone in the forest and pursued by angry Germans.
Wiesniewski is treated by Dr Ray Garcia, and finds that he is already starting to forget the odd experience he had before meeting the Doctor. Although he’d thought the bodies of his men were disappearing and that he’d encountered terrifying creatures, all he can remember now is a mist and animals he thinks were deer -- except for a vague impression that they were bipedal. The Doctor is unable to convince Colonel Lewis to release the equipment he needs to get the TARDIS out of the river, and with no other choice open to him he agrees to help Garcia at the hospital. The body of a man suffering from third-degree burns has disappeared, and although Garcia puts this down to a paperwork snafu, the Doctor notes the parallel to Wiesniewski’s story. Lewis, meanwhile, summons Wiesniewski and orders him to clamp down on the rumours of odd occurrences, which he claims are bad for morale; but while walking past Lewis’ office later, Wiesniewski hears him apparently talking to himself and gets the strong impression that, despite the evidence, there is in fact someone else in the room...
Garcia catches Kovacs selling food on the black market, but Kovacs convinces him that it’s just extra food overstocked by the catering corps which would otherwise have been thrown out; Garcia agrees not to turn him in, but Kovacs now owes him a favour. Bearclaw is brought in, suffering from exposure and delirium, telling of the massacre at the Baugnez crossroads -- and Sam’s death and disappearance. The horrified Doctor leaves to think things over and finds himself suddenly transported to a forest glen, where a beautiful woman tries to seduce him. When Garcia finds the Doctor, no subjective time has passed, although the Doctor apparently spent quite some time in the other world. As they return to the hospital, Bearclaw sees what appear to be doctors in surgical gowns -- who appear to be floating some way above the ground. The floating surgeons gather around a mortally wounded man, and seem to dwindle into the distance without moving. By the time Garcia can wrap his mind around what he’s seeing, the “surgeons” and the patient have vanished.
Sam awakens to find herself in another world, with a strange, silky type of flesh replacing the wounds in her skin. At first she believes that she’s died and been taken to Mictlan, home of the Celestis, but one of her hosts, a Sidhe named Galastel, assures her that they got to her first. Galastel takes her to the city of the Sidhe, where she sees that a dimensional rift has caused the war to impact upon these higher realms as well. Titania, queen of the Sidhe, orders Galastel to teach Sam how to use her new perceptions of the higher dimensions, and Galastel takes her back in time to witness her arrival. She is surprised to see that, from her new perspective, the TARDIS appears more organic and the Doctor somehow more real than anything else in the vicinity. Galastel explains that the Sidhe have the power to cloud men’s minds and pass among them unnoticed, and demonstrates by convincing Sergeant Kovacs that Sam isn’t a spy even though he’s seen no papers to prove it.
The Doctor’s suspicions that Sidhe are involved are confirmed when the beautiful woman, Titania, contacts him again to ask for his help. The Sidhe evolved on Earth alongside humans, but their perceptions stretch through all eleven dimensions rather than the four to which humanity is confined. Long ago, humanity and the Sidhe formed an uneasy truce, but over the years, humanity has forgotten the Sidhe, consigning them to myth and legend. The Sidhe, however, will stand for no more breaking of the truce, and have already begun to kidnap the nearly-dead and transform them into Sidhe in order to replace those Sidhe killed by the damage caused by the human war.
Wiesniewski overheard Lewis talking about learning something from the failure in Philadephia, and the Doctor suspects that he’s referring to the Philadelphia Experiment, in which the USS Eldridge vanished from the face of the Earth in an attempt to make it radar-invisible; perhaps it phased out of the normal dimensions and put Lewis in contact with the Sidhe. When Fitz arrives with his story, the Doctor realizes that Lewis and Leitz are working together with the aid of Oberon, king of the Sidhe. The Sidhe worship the forces of order and chaos, and where Titania represents order and stability, Oberon represents chaos and anarchy. As such he cannot be held responsible for his actions, and he is interfering in the human war just for the sake of it. With his help, Leitz and Lewis have developed electromagnetic generators to phase tanks into higher dimensions, and they intend to fight a battle in the Sidhe’s realm to see if it is possible to do so. Leitz, knowing that the German war effort is doomed, hopes to escape to the West after Berlin falls, and to use his knowledge to bargain for a position amongst the Western military and help fight the war he is sure will follow against Russia. But the Doctor knows that if humans bring their war directly into the realm of the Sidhe, the Sidhe will react against the breaking of the truce and declare war upon humanity.
The Doctor confronts Lewis, who is shocked to see that the Doctor does not cast a shadow and agrees to lend him the men he needs to recover his “equipment”. Having been warned about the Doctor by Oberon, however, Lewis refuses to lend the Doctor any equipment, hoping that he will be killed when he enters the combat zones. Garcia calls in his favour from Kovacs to lead them into contact, and the Sidhe get them close to the German lines; there, they attack and capture a German tank, and the Doctor tricks two pursuing tanks into firing upon each other. He and his allies are then able to dredge the TARDIS out of the river. Sam, meanwhile, has Galastel lead her to the rift, which turns out to be a minor anomaly being worsened by the presence on Earth of the dimensionally-shifted Beasts -- the parasites she and the Doctor encountered when they first met Fitz. As the rift is electromagnetic in nature the Doctor can seal it with two thousand tonnes of metal, but Lewis and Leitz are already heading for the rift with their specially augmented tanks, and once they cross over the truce will be broken.
The Doctor sends Wiesniewski, Kovacs, Bearclaw and Garcia to help the Sidhe hold off the two forces for as long as possible, while he takes Sam and Fitz to the site of the Philadelphia Experiment and materializes aboard the misphasing Eldridge. As he connects a cable from the TARDIS to the Eldridge, however, he finds degaussing equipment aboard, which would make it possible for a Sidhe to move aboard the iron ship; it appears that Oberon has anticipated their move and travelled back in time to stop them. Indeed, “Sam” turns out to be Oberon in disguise, and he attacks the Doctor. The Doctor realizes that Oberon, traditionally unable to be held responsible for his actions, is trying to see just how far he can go. The Doctor thus has no choice but to destroy the degaussing equipment, trapping Oberon on the Eldridge, unable to phase out through solid iron. The Doctor and Fitz then retreat to the TARDIS and transport the Eldridge into the rift.
The Doctor’s human allies block off the roads to the rift, and Wiesniewski and Garcia contact the American soldiers and convince them that Lewis has done a deal with the Germans. Lewis catches them and kills Wiesniewski, accusing him of treason. Bearclaw and Kovacs, meanwhile, capture a German tank and run over Leitz, killing him. Having disposed of the augmented tanks, they then lure two German tanks through the woods after them to the American forces, where the Germans open fire, killing Lewis and destroying the abandoned augmented American tanks. The Eldridge then materializes in the rift, short-circuiting it and killing the trapped Oberon in the process. Garcia is stabbed to death by a German soldier even though the battle is already over. Sam decides to remain in human phase, to Galastel’s disappointment, and as she, Fitz and the Doctor return to the TARDIS, Sam asks the Doctor to drop her off the next time they arrive in 1997. After all of the changes she has experienced, she is now self-confident enough to start making a difference in her own world, and she’s ready to go home.