As the team emotionally struggle to recover from the aftermath of Helen's attack, Jenny leads the team to a new Anomaly at an airport; where a Giganotosaurus or "G-Rex" threatens the crew of a Boeing-747, a news crew are attempting to document the incursion for the media, and Danny Quinn gives the reluctant team his unwanted help.

Jenny and the team, with unwanted help from Danny, attempt to stop London from becoming engulfed by a pandemic when they face an incursion of a deadly, fast-spreading fungus from the future that turns its hosts into primal monsters. Meanwhile, Sid the Diictodon has escaped Connor's custody into the ARC and is causing calamity, and Jenny learns the truth about Claudia Brown.

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.

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.