A year after becoming marooned in the past, Connor and Abby return from the Cretaceous to a changed and upgraded ARC, but Connor accidentally brings a Spinosaurus back to the present with them.

While Connor and Abby try to earn their old positions on the team back, Connor reunites with his old friend Duncan, who leads Connor to a series of homeless killings at a dock area that the team discover are the work of an elusive and deadly Kaprosuchus.

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.

The team go to investigate a flunctuating Anomaly signal at a seaside village, and Matt and Abby struggle to contain a fast and deadly Labyrinthodont's rampage while Connor tries to uncover the secret behind the fluncuating Anomaly signal. Meanwhile, Emily has been captured by Ethan, and Matt attempts to track and save her before it's too late.

The team investigate an Anomaly incursion at a rural manor house, and reunite with Jenny and discover that the manor is the location for her wedding in the morning; forcing the team to contain a pack of Hyaenodon while ensuring Jenny's soon-to-be-husband doesn't find out. Meanwhile, Jess and Becker are caught in Ethan's deadly trap.

The team head to an old prison, where they discover an Anomaly that won't lock and is producing satellite Anomalies throughout the prison, which in turn makes it even harder for the team to track a Terror Bird loose in the prison. At the same time, Danny returns from the past with a warning for the team, Ethan's true identity is discovered, Emily is torn between Matt and the chance to return to her home, Matt reveals his secret, and Connor makes a terrible discovery.

The team attempt to track a giant, underground insectoid predator from the future, and there is something about the creature that Matt isn't telling the team. Meanwhile, Philip shows Connor the true purpose behind New Dawn, and Abby becomes more suspicious of Matt and grows closer to discovering his secret, while Lester struggles at the ARC to make a good impression to Ms. Reece of the Cabinet Office for a knighthood.

When a Navy submarine in the North Sea discovers a giant underwater Anomaly, Matt, Connor and Abby join the Navy crew aboard, but things go awry when the submarine is pulled through the Anomaly into a prehistoric sea inhabited by giant pliosaurs. The team subsequently attempt to get the submarine back through the Anomaly to their time, while Lester struggles to stop an Admiral from nuking the Anomaly and potentially altering history.

When the team send a Raptor at an art museum back through the wrong Anomaly, Matt goes through into Victorian London in pursuit of the Raptor, and there he reunites with Emily and attempts to help her escape her grim fate of incarceration at Bedlam Asylum by her shallow husband. Meanwhile, Abby infiltrates Connor's lab to capture Connor's files on New Dawn for Matt.

The team learn the truth about New Dawn when Connor creates an artificial Anomaly in the ARC, and trouble soon erupts when the Anomaly unleashes swarming, carnivorous beetles from the future into the ARC, which trigger the lockdown but threaten to burrow out and swarm onto the modern world. The situation is only exacerbated when the beetles trigger Jess' deadly allergy to insect bites, and when Philip threatens to incinerate the entire ARC to stop the beetles.

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.