After returning from the past to find that Claudia Brown has been erased from time, Nick Cutter is forced to cope with other changes, including that the team are now their own Anomaly-combatting organisation called the Anomaly Research Centre. Just when Cutter finally begins to come to terms with losing Claudia, a new PR guru joins the ARC; Jenny Lewis, who is physically identical to Claudia Brown but temperamentally is a completely different person.

Meanwhile, though Cutter believes that Stephen has gotten over Helen's betrayal, Stephen has in fact begun seeing Helen again and is becoming torn between her and Cutter; while Connor begins dating the mysterious Caroline Steel. Abby doesn't trust Caroline, and her and Connor's opposing opinions on her begin to drive a wedge between them. Unbeknownst to anyone, Caroline is secretly spying on Connor for the mysterious Oliver Leek, who has a secret agenda of his own for the Anomalies alongside Helen.

After the ARC team learn of Leek's and Helen's secret plans to use a creature army that they have captured to create chaos in the present, they are forced to try and stop the creatures from escaping onto the modern world. Helen, Nick and Stephen manage to trap and kill the creatures, but Stephen loses his life in the process. In the aftermath, Cutter finally accepts that Claudia Brown is gone forever and moves on with Jenny, while Helen promises that things will change with her clone army.