Dartmoor, 2002. Vampire hunter Nimrod returns to the Forge with Cassie Schofield, the young woman who was transformed into a vampire by Amelia Doory’s Twilight virus. Months of isolation and fear have turned Cassie into a feral killer, who rips out the throat of a new Forge recruit named Private Mark Bradley when he gets too close to her. To Nimrod’s dissatisfaction, Deputy Director Crichton orders him to train Cassie, condition her, and enlist her as an operative for the Forge. Dr Edith Crumpton supervises the operation as Nimrod starves Cassie nearly to death and then uses direct cerebral stimulation to alter her memories. Soon, she will forget the existence of her son Tommy, she will believe herself to have killed Evelyn Smythe, and she will accept further brainwashing and become a Forge operative.
Lapland, present day: A fireball falls from the sky near the Sami village of Utsjoki. Soon afterwards, a young boy named Otto Somby is attacked and torn apart by a monstrous figure lurking in the woods. Otto’s grief-stricken father, Jukka, heads out into the tundra with his friend Urso, and they find the twisted wreck of a spaceship; when they touch it, they briefly short out an energy field around its hull, and something emerges from the ship and tears them apart. Back at the village, a strange illness begins to spread, causing its victims to mutate into monsters.
The Forge detects the crash in Lapland, and Major Kirby of Whitehall orders Nimrod to send in an extraction team. Nimrod orders Crumpton and Sergeant Frith to accompany him. Meanwhile, two innocent backpackers, John and Patricia, happen to wander off their hiking trail and onto the grounds of the Forge -- and when Nimrod sends Cassie along with the team to deal with them, she attacks the hikers without provocation and slaughters Patricia before John’s eyes. Frith and his team take John in for brainwashing; he will be released believing that he went mad and killed his own wife. Frith is infuriated, but Nimrod, pleased by Cassie’s instinctive killer reaction, decides to take her along on the mission to Lapland.
When the extraction team arrives in Lapland, Cassie tests her growing telepathic powers and is nearly overwhelmed by a powerful sense of alien evil. As she recovers, the team reaches Utsjoki, only to find the village deserted apart from a frightened 11-year-old boy named Iver who claims that his fellow Sami have changed. A monstrous humanoid figure then surprises Private Longworth and tears him apart; bullets only slow it down, but Nimrod’s crossbow kills it. Crumpton conducts an autopsy and identifies the monster as the village doctor, Matti Jackiesson. The crashed ship is emitting a strange form of radiation, and although the extraction team members are protected by their BAN suits and anti-radiation drugs, the villagers seem to have been transformed into alien hybrids. Jackiesson’s behaviour implies that he was taking Longworth’s body apart to see how it worked. Iver also transforms into one of the monsters and kills Private Kirk, and Corporal Lysandra Aristedes is forced to shoot and kill the 11-year-old boy.
Despite objections, Nimrod takes a helicopter out to the crash site; on the way, he sees the mutated Sami all heading in the same direction and theorises that the alien ship has transformed them into a repair team. When the helicopter arrives, a radiation surge causes it to crash into a force field around the ship; fortunately, the explosion briefly shorts out the force field, and Nimrod survives and lands on the opposite side of the field. While the extraction team heads out to the ship, Nimrod finds himself under psychic assault by something that seems to be trying to take over his mind. Rather than wait for the others to find a way through the force field to rescue him, Nimrod plants explosives on the ship’s hull and disables the force field himself; however, the sense of triumph he then feels is not his own, and he realises that the alien intelligence that’s been attacking him successfully manipulated him into shutting down the force field.
Nimrod takes Crumpton, Aristedes and Private Dann into the ship to investigate further, while Cassie remains outside to help Frith and his men when the Sami mutants arrive and attack them, trying to get to the ship. However, she is also assaulted by an alien mind, and when she experiences its memories she learns that it is named the Nyathoggoth. Inside the ship, while Crumpton examines the central computer core with a portable Oracle unit, Nimrod, Dann and Aristedes explore further; however, Dann is attacked and torn apart by a sentient liquid, the Nyathoggoth’s physical form. The Nyathoggoth heads to the surface, where the Sami villagers stop trying to reach the ship and instead turn on the Nyathoggoth. It is too strong for them, but as it tears its way through the Sami and the Forge soldiers, Cassie realises that it is feeding off their blood. She thus allows it to attack her, and although Frith “rescues” her before he realises what she’s doing, the creature drinks enough of her blood to become infected with the Twilight virus. As it struggles to fight off the infection, Frith and his men prepare to evacuate.
Crumpton manages to interface the Oracle unit with the ship’s systems, and by the time Nimrod and Aristedes return, she’s learned that the ship is a maximum-security prison for the Nyathoggoth -- a creature that slaughtered entire worlds to satisfy its hunger for blood. Billions died before the Nyathoggoth was contained in this ship, which was programmed to fly directly into a black hole; however, something went wrong and the ship crashed on Earth, where its automated systems sent out the radiation that transformed the villagers into a repair team.
When Nimrod grasps the scale of the devastation caused by the Nyathoggoth, he concludes that the Forge is out of its depth and that the creature must be destroyed. However, the Oracle unit refuses to help him, as it has been programmed to harvest xenotech, not destroy it. Nimrod -- part man, part vampire, part machine -- tears the Oracle unit free of the ship’s computer, connects himself in its place, and initiates the ship’s self-destruct sequence. On Aristedes’ suggestion, he also programmes the containment field to raise itself again after the Forge team have escaped, hoping that this will hold in the radiation when the ship explodes.
Exhausted, Nimrod leads Aristedes and Crumpton out of the ship, but the Nyathoggoth takes over Cassie’s mind and tries to kill Nimrod through her. She successfully defeats him in a one-on-one battle, but at the last moment, her personality resurfaces and she stabs herself rather than him. As the extraction team evacuates, the Nyathoggoth speaks to Nimrod through Cassie, offering him the power of a god if he joins it -- but Nimrod refuses the offer, and when the ship explodes, the Nyathoggoth is destroyed.
Back at the Forge, the recovering Cassie reveals that she knows Nimrod has tampered with her memories and that Evelyn Smythe is still alive; however, she still doesn’t remember the existence of her son Tommy. Crichton’s term as Deputy Director is over, and he’s looking forward to a peaceful retirement, unaware that Nimrod’s first act as the new Deputy Director has been to order Crichton’s assassination. The people of the Forge continue their work, but in Lapland, a trace of the Nyathoggoth remains alive...