Eight years after his wife Helen mysteriously disappeared, Nick Cutter and a team of several others investigate reports of a large animal in the Forest of Dean, and discover that mysterious Anomalies in time and space are appearing and allowing prehistoric creatures to cross into the present day.

When a pest controller is attacked in the London Underground and landed in hospital poisoned with venom, Cutter, Claudia and the team investigate and discover the Underground is infested with giant, Carboniferous spiders. Cutter and the team soon learn that the true culprit is not the spiders, but a giant centipede, and they are sent in a race against time to get the centipede's venom after it poisons Stephen.

Meanwhile, Connor gets thrown off the team after telling two of his friends about the Anomalies, and attempts to earn the team's faith back in the fight against the giant centipede. At the same time, Cutter's suspicions that Helen is alive on the other sides of the Anomalies increases.

The team are called in to investigate when a lifeguard is eaten by a Mosasaur at a swimming pool. Cutter discovers that they are dealing with a mobile Anomaly when the Mosasaur and the lifeguard's vomited remains appear at a reservoir and a cellar floods and is invaded by a Hesperornis. The rest of the team also learn that Helen is alive and on the other side of the Anomaly, and so Cutter is forced to go through and confront the woman his wife has become.

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.

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.

When an Anomaly opens at a theatre, a group of mysterious Anomaly travellers come through, followed by fast and deadly Tree Creepers. Meanwhile, Connor helps Philip design a new security system for the ARC, but it goes horribly awry and sends the ARC into lockdown, and time is running out for Connor to free Rex and Philip before the system suffocates them.

Matt, Connor and Becker investigate an Anomaly at a secondary school and struggle to save the remaining students from deadly, venomous Therocephalians. Meanwhile, Philip decides to have the ARC's captive creatures including Rex euthanized, prompting Abby to try and smuggle them to safety before it's too late.

With Convergence having finally arrived, while Becker and the entire ARC struggle to contain an increasing outbreak of numerous Anomalies and creatures, New Dawn begins to power up for its final phase, as the team struggle to stop Philip from activating New Dawn before it's too late.

Matt and Abby go through New Dawn's Anomaly on a rescue mission for Connor into the barren, Predator-ruled wastelands of the future, while back in the present, the future apocalypse looms closer as New Dawn spirals out of control. Meanwhile, Jess and Lester face problems of their own when the ARC is invaded by Mutated Future Predators.