Series 2 focuses on the effects on the relationships of, and emotional challenges on the team (primarily Nick Cutter's struggle to cope with losing Claudia Brown), and on Helen Cutter's and Oliver Leek's mysterious plans.
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-combating 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.
Episode 1: As Cutter tries to come to terms with Claudia Brown's disappearance, he struggles to adjust to working with her replacement, the slimy Oliver Leek (Karl Theobald). Meanwhile, bloodthirsty raptors are rampaging through a shopping mall and the team are called in to deal with the situation. When the team arrives back at the ARC, they are introduced to Jenny Lewis (Lucy Brown), the ARC's new PR officer, and a doppelgänger of Claudia Brown.
Episode 2: Cutter and his team find themselves pursuing giant, carnivorous worms that start to appear through an eerie fog in a local office block after emerging through another anomaly. As the team deals with the problem, Cutter becomes preoccupied with the team's new PR executive, Jenny Lewis, whom he is convinced is actually Claudia Brown.
Episode 3: Connor's new anomaly detector is set up in the ARC, but there are fears that the device will not work when another violent attack is reported at Blue Sky amusement park. Investigations lead the team to deduce the attacks took place before the detector came online. The team discover a Sabre-toothed cat is roaming the park, killing at will, but as their hunt continues, they begin to suspect someone knows of the creature's presence and is covering up for it.
Episode 4: After a teenager mysteriously disappears, the team investigate, and narrowly save Jenny from death at the jaws of a highly unusual shark lurking in the River Thames. Cutter is convinced that the shark's unique morphology is the result of further evolution – that it's a species from the future. They then split up to find the creature's lair but trouble brews when Abby Maitland (Hannah Spearritt) is dragged through an anomaly by another carnivorous species from the future: the Mer.
Episode 5: A young girl searching for her dog ends up stuck on the other side of an anomaly, leading Cutter and Stephen to mount a rescue mission into the sandy deserts of the Silurian. But when the anomaly closes, the trio end up trapped with a horde of giant Silurian Scorpions which track them from hearing vibrations in the sand. As the three of them fight for survival, Cutter realises they are not alone: someone is actively trying to sabotage their work.
Episode 6: A Columbian Mammoth slips through an anomaly, rampaging along the M25 scattering cars and lorries in its wake. As Cutter, Abby, Connor and Jenny take on the task of stopping it, Stephen is shocked when Helen returns with plans of her own. After taking the mammoth back to the ARC, Cutter decides to set a trap to root out the traitor in their midst, leaving Lester to fight for his life against a Future Predator that has infiltrated the ARC.
Episode 7: Cutter and the team are kidnapped and held in a military bunker by Oliver Leek, who has plans to be the most powerful man in the world using an army of fearsome predators he has captured from past anomalies, while his ally, Helen, furthers her own nefarious schemes. As the team fight for their survival, Stephen deals with a Silurian Scorpion which Leek has unleashed onto a busy beach. Back at the bunker, the team have found a way to stop Leek, but at the cost of Stephen's life.
Best Episode: Episode 4/5
Worst Episode: Episode 6