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.

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.