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.

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.

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.