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.
The team investigate when an Anomaly opens in an Ancient Egyptian artefact at the British Museum, and when a Pristichampsus comes through, Cutter, Abby and Jenny are sent into a race after the giant crocodilian through Central London. Meanwhile, Connor and sparky Egyptologist Sarah Page discover that the Anomaly, the artefact and the creature hold an incredible ancient secret.
Cutter's new Anomaly predictions lead Jenny, Connor and Abby to a reputedly haunted abandoned house, where they soon learn that the Anomaly incursion dates back fourteen years and the house is inhabited by a deadly Camouflage Beast. The team also have to deal with the antagonistic suspicions of Detective Constable Danny Quinn on their interest in the house.
Cutter and the team head to a hospital to deal with an Anomaly and a Diictodon colony wreaking havoc on the hospital's power supply, and also have to help deliver a baby and stop a greedy journalist from getting proof of the creatures. Meanwhile, Helen Cutter and her clone army launch their attack on the ARC, and Helen reveals a secret about the future to Nick.
As the team emotionally struggle to recover from the aftermath of Helen's attack, Jenny leads the team to a new Anomaly at an airport; where a Giganotosaurus or "G-Rex" threatens the crew of a Boeing-747, a news crew are attempting to document the incursion for the media, and Danny Quinn gives the reluctant team his unwanted help.
Jenny and the team, with unwanted help from Danny, attempt to stop London from becoming engulfed by a pandemic when they face an incursion of a deadly, fast-spreading fungus from the future that turns its hosts into primal monsters. Meanwhile, Sid the Diictodon has escaped Connor's custody into the ARC and is causing calamity, and Jenny learns the truth about Claudia Brown.
When Johnson takes Lester's control over the ARC, the team are forced to flee into hiding from Johnson's forces at an abandoned rural military outpost, where they come under attack by a pack of bloodthirsty Terror Birds.
Danny and the team face a Medieval-esque incursion when a Dracorex comes through an Anomaly pursued by a Medieval knight, who - believing he has followed the creature into Hell - causes calamity around modern London as the team try to reason the truth to him. Meanwhile, Connor tries to buy Rex back from Jack's greedy friend.
Jack searches for answers about Abby's secret life, and gets chased through an Anomaly by a deadly Megopteran; forcing the team to go through on a rescue mission into the desolate, predator-filled ruins of the future.
While the rest of the team deal with a herd of Embolotherium that threaten a rural racing campsite, Danny goes on an infiltration mission to rescue the mysterious Eve from Johnson's forces. But when the team soon discover who Eve really is, her rescue from Johnson has disastrous consequences.
While Sarah and Becker deal with a Megopteran attack at Johnson's old HQ, Danny, Connor and Abby return to the future to stop Helen; the trio soon learn the truth behind Helen's master plan, and are sent on a race through the Anomalies to stop her before she ends humanity at its beginning.