While Stephen deals with a Silurian Scorpion attacking a popular beach resort, the team are trapped in Leek's bunker with an army of creatures. When the creature army escape and run amok in the bunker, the team must both escape the overrun bunker with their lives and stop the creature army from escaping onto the modern world.

The team are sent to deal with a Columbian Mammoth rampaging on the M25, and attempt to save a trapped motorist before she frightens the Mammoth into attacking again. Meanwhile, Connor and Abby search for the missing Rex and Caroline, and Stephen reveals his alliance with Helen Cutter. Connor and Cutter spring their trap to find the traitor in the ARC, and Oliver Leek's true colours are exposed and the team race to track him down.

As Cutter struggles with losing Claudia Brown and with the other consequences of the failed mission into the past and tries to get the team to see that history has been altered, the team are sent to a shopping mall to contain an infestation of deadly, ruthless Raptors. Arguments among the team intensify when Cutter wants all the Raptors tranquilised and sent back through the Anomaly alive.

When a boy's disappearance down a drain coincides with an underwater Anomaly, Stephen and the ARC search the local canal for the aquatic predator behind the disappearance, while Cutter is convinced the creature is somewhere else. Cutter turns out to be right in the worst possible way when Abby is taken by Mer Creatures from the future and held captive in a flooded warehouse cellar. Meanwhile, Cutter and Connor learn that there is a conspiracy within the ARC.

When a young London girl chases her dog through an Anomaly into a harsh, prehistoric desert world, Cutter and Stephen go through on a rescue mission for the girl, but find themselves up against giant sand scorpions. The team's problems only worsen when the Anomaly closes on the trio and leaves them marooned in the hostile desert world.

Cutter struggles with the arrival of the ARC's new PR guru, Jenny Lewis, who is physically identical to the lost Claudia Brown, yet is temperamentally a completely different person with no idea of her doppelganger; while Connor gets picked up by a beautiful young woman who is everything he is not, but Abby and Rex are both suspicious of her; and Stephen begins seeing Helen again. When an Anomaly releases a yellow, sulphuric mist inhabited by giant, carnivorous worms on a gleaming new high-rise office block, Cutter and Stephen are sent in to deal with the deadly creatures with Jenny, while back at the ARC, Connor and Abby try and find a fog-battling weapon.

Connor builds the team a new device designed to detect and locate new Anomalies, but the team become doubtful that the device works when it detects no Anomaly when a paintballer is torn to shreds in the luxurious Blue Sky Park resort. The team soon learn that the mysterious predator stalking the Park is a powerful and deadly sabre-toothed cat, and the race is on to find who is harbouring and protecting the sabretooth before it kills again.