Series 3 focuses primarily on the ARC team, as they go through numerous changes and challenges; including the death of Nick Cutter, the attempts of Christine Johnson to take control over the ARC, and Helen Cutter's attempts to destroy the ARC to try and save the future.
As the ARC team still reel from Stephen's death, they are joined by several new team members, including new security leader Captain Hilary Becker, and sparky Egyptologist Sarah Page. Meanwhile, after discovering a future world where the Earth is overrun with Future Predators, Helen Cutter sets out on a mission in the present against the ARC, whom she blames for the future catastrophe, and launches an attack on the ARC in which Nick Cutter is killed by Helen.
The ARC subsequently manage to obtain a mysterious artifact from the future from Helen, which in turn causes military liaison Christine Johnson to target the ARC and attempt to take control of it and get the Artifact for her own purposes. Following Cutter's death, the ARC team are ultimately joined by ex-cop and new team leader Danny Quinn, and Jenny Lewis learns of her alternate life as Claudia Brown and ultimately leaves the ARC. Meanwhile, Connor himself is forced to move out of Abby's flat and into Lester's (to the latter's chagrin and misery) when the troublesome Jack Maitland moves in with Abby.
As Johnson's mission to get the Artifact from the ARC continues, Helen returns and kills Johnson. When the ARC team learn that Helen intends to wipe out humanity's ancestors to stop them evolving to cause the future disaster, Danny, Connor and Abby are sent on a race after her through the Anomalies. Helen is killed before she can kill off enough of humanity's ancestors to have a temporal impact, but Abby, Connor and Danny are themselves left marooned in the past.
Episode 1: An exhibition of ancient Egyptian relics comes to the British Museum and an anomaly opens in a mysterious monument called the "Sun Cage". A Pristichampsus, believed in Ancient Egypt to be the demon Ammut, emerges and proceeds to wreak havoc in London. Cutter, Abby, Jenny and new security chief, Captain Becker (Ben Mansfield), pursue it through the city while Connor and new recruit, Egyptologist Sarah Page (Laila Rouass) try to stop more creatures coming through, and make some interesting discoveries about anomalies in the process. Meanwhile, Lester encounters a new adversary: the devious and ambitious Christine Johnson (Belinda Stewart-Wilson), who is after a strange artifact that Helen has stolen.
Episode 2: Three teenage boys break into a house and a "Gremlin" (a future beast able to camouflage itself in any environment) attacks them. Only one boy manages to escape alive. Fourteen years later, in the present-day, Cutter predicts an anomaly will appear in the same house the boys were killed. He sends Jenny, Abby and Connor to investigate. However, their efforts are thwarted by the creature and the attentions of detective Danny Quinn (Jason Flemyng), who is investigating his brother's disappearance 14 years before. Meanwhile, Cutter, Becker and Sarah are caught off-guard when Helen's forces attempt to infiltrate the ARC.
Episode 3: An anomaly opens at the West London Hospital, causing cute but dangerous Diictodon to emerge. They promptly chew through the power cables, cutting the power to the building. Cutter, Abby, Connor and Becker arrive to investigate and evacuate the building as does journalist Mick Harper (Ramon Tikaram) from Evening News HQ, who wants to get evidence of the creatures to expose to the public. However, they return to find Helen and her Cleaner Replica troops (including a clone of Cutter) have taken over the ARC, so they can interrogate the real Cutter about the artifact. As a bomb blast tears the ARC apart and the team battle for survival, Helen declares that she must stop the ARC'S research from destroying the world at any cost... even if it means killing her husband.
Episode 4: Mick Harper steals an anomaly detector from Jenny's car and uses it to track down an anomaly at an airport, bringing Nigel Marven with him to identify any creatures that come through. Yet when a Giganotosaurus from comes through the anomaly, the team has to not only stop the bloodthirsty dinosaur destroying the airport and a nearby aircraft, but prevent the journalists broadcasting its existence to the world. Danny Quinn appears and helps them, then refuses to leave.
Episode 5: Danny Quinn breaks into the ARC and is drafted in to help the team when a fast-growing flesh-eating fungus from the future is transferred to the present and infects a businessman, Sir Richard Bentley. Danny arrives with flamethrowers to try and burn Bentley as he is already infected not realising fire doesn't work. The team manage to bring the creature back to the ARC to destroy it, where Jenny is trapped in the freezing cold main operations area with it and forced to fight for her life. After her recent discovery of Cutter's picture of Claudia Brown and her near-death experience, Jenny decides that she's had enough: she resigns from her job at the ARC, leaving Danny in charge of the team.
Episode 6: With Jenny Lewis's departure and Nick Cutter's death, Danny Quinn is made the new leader of the team. When Christine Johnson and her soldiers take over the ARC in search of the artifact, the team escape to an old cabin on Ministry of Defence property within a minefield which has been abandoned since the 1930s. As Johnson ousts Lester and imposes her will on the ARC staff, Becker must find a way to defeat her. At the same time, with no weapons but their own initiative, Danny, Connor, Abby and Sarah have to find a way to defend themselves, not only from Johnson's soldiers, but from a pack of rampaging terror birds that emerge from a nearby anomaly.
Episode 7: A Dracorex comes through an anomaly, trying to escape from a 14th-century knight who believes he is hunting a dragon. The team are forced to find and save the life of the Dracorex, and then, aided with a bit of medieval research by Sarah, return the confused knight, who thinks he is a new Saint George, to his own world before he kills anyone, out of belief they are demons and he is in hell.
Episode 8: An anomaly opens at a race car test track and a Megopteran, an insect from the future, comes through. It is carnivorous and lethal, and the team must draw on all their resources to get it back to its home. However, things get complicated when Jack (Robert Lowe) decides to find out what his sister Abby really does for a living, and inadvertently drives through an anomaly into the future: a post-apocalyptic world overrun by Future Predators. Now the team must mount a desperate rescue mission after Jack, and then find a way to escape with their lives.
Episode 9: The team have to deal with a herd of Embolotherium from the Eocene. Danny arrives with a mysterious woman called Eve who he first saw in the future; having rescued her from Christine Johnson, they endeavour to save everyone from the stampede. When the anomaly closes, at a campsite, Eve opens another anomaly to return the beasts and are all saved. Upon their return to the ARC, the team are shocked to discover that Eve is Helen Cutter in disguise, who takes Johnson hostage. Holding her at gunpoint, Helen steals the artifact, pushes Johnson through an anomaly to be butchered by Future Predators, and vows once again to stop the ARC's work from destroying the world. The team decide they must stop Helen before she kills anyone else.
Episode 10: Sarah and Becker investigate an anomaly that re-opens at Johnson's HQ and end up fighting for their lives against Megopterans, while Danny, Abby and Connor hunt for Helen in the future. The trio discover Helen plans to prevent the evolution of mankind in order to save the world, resulting in a chase across Cretaceous North America and into Pliocene Africa. Danny confronts Helen at the location of the human ancestor, Australopithecus, only to find she has poisoned a small group already. Helen delights in her apparent victory, but a Raptor that followed Danny through the anomaly charges at Helen and knocks her off a cliff, killing them both. Having ensured the other hominids have survived, Danny then makes his way back to the anomaly, but it vanishes just before he reaches it.
Best Episode: Episode 2/5/6/8
Worst Episode: Episode 4