Eight years after his wife Helen disappeared, evolutionary zoologist Professor Nick Cutter - along with his friend Stephen Hart, his geeky student Connor Temple, zookeeper Abby Maitland, Special Forces leader Captain Tom Ryan, and government officials James Lester and Claudia Brown - discovers that mysterious rifts in time and space called Anomalies are allowing creature from across Earth's history to run rampant in the present; and the group subsequently become a Home Office research team tasked with predicting the Anomalies and containing the ceatures which come through them, and learning more about the Anomalies and why they are happening.
However, Cutter secretly has an agenda of his own about the Anomaly operation: as the team investigate the Anomalies, Cutter begins to find more clues that imply his long-missing wife Helen is alive and living in the past on the other sides of the Anomalies. The rest of the team eventually learn of this, and that Helen is indeed alive and in the past, but she has been greatly changed by her time there and her study into the Anomalies, and the team are uncertain which side she is on. Eventually, Helen seemingly allies with the team to find and contain an Anomaly in the past to the future and to combat a deadly predator from the future which is on a killing spree in the present; but while Nick and Helen are searching in the past for the future Anomaly, Nick discovers that Helen only wanted to find the Anomaly and see the future, and after Captain Ryan is killed, Nick returns to the present. However, there, Cutter finds that Claudia Brown has been erased from the timeline while he and Helen were in the past.
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.
Helen Cutter directs the team to an Anomaly at a football stadium and escapes through, leaving behind a flock of Dodos. The team soon discover that the Dodos are host to a deadly parasite, and struggle to stop a pandemic when Tom is infected and - convinced that the government are incubating a mind-controlling biological weapon inside him - goes on the run from the team.
The team investigate the brutal death of a golfer at a golf course, and discover an aerial Anomaly and a Pteranodon in the skies above. Claudia is convinced that the Pteranodon is responsible for the golfer's death and wants deadly force used against it, but Cutter and Stephen are convinced otherwise. Cutter's suspicions are confirmed correct when Claudia is trapped in the golf course's clubhouse by a deadly, flesh-eating swarm of Anurognathus.
Meanwhile, Connor accidentally frees Rex from Abby's flat, forcing Abby and Connor to chase Rex across the golf course.
When the original Anomaly in the Forest of Dean reopens and a string of disappearances plague the area, Helen Cutter returns with a warning for Nick Cutter and the team about the deadly, elusive new predator the team are struggling to track: it is not a creature from the past, but from the future. Nick and Helen both want to go on an Anomaly containment mission into the past to stop the future from altering it, which ends in terrible consequences.