After a year marooned in the Cretaceous, Connor and Abby finally return to the present to find that the ARC has greatly changed in their absence, and is now funded by entrepreneur Philip Burton and led by the quiet and mysterious Matt Anderson. Connor and Abby are initially not allowed back on the main team due to a new military code, but soon manage to get back on, though they still have to try and earn their old positions on the team back.
When two Anomaly travellers (the Victorian lady Emily Merchant and the murderous Ethan Dobrowski) come to the present, Matt takes Emily in, and begins to open up to her on his past and who he really is, while hunting Ethan and trying to protect Emily from him. Meanwhile, Connor becomes more and more allied with Philip and the latter's mysterious New Dawn project for the Anomalies, and Connor and Abby's relationship begins to become strained because of this.
Eventually, Danny Quinn returns from the past as well, and Ethan is revealed to be Danny's long-lost brother Patrick. Both Danny and Ethan/Patrick return to the past, and Emily returns to her time as well; but not before Matt reveals to her that he is from the future and has been sent back to stop an apocalyptic disaster with the Anomalies in the present from destroying the planet. Meanwhile, Connor learns of a catastrophic upcoming event with the Anomalies, and ultimately allies with Philip and New Dawn against it.
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.