Back at the university, Connor Temple is trying to convince his two friends, Tom and Duncan, about the anomalies and the prehistoric creatures he saw, although the government warned him not to and although he had signed under the Official Secrets Act. They both laugh at him and dismiss his claims. Later, when going through a web site about supposed official conspiracies Connor finds what looks like another anomaly sighting in the New Forest.
Abby Maitland and Rex are at her home. Connor Temple arrives with reports of another anomaly and discovers that Rex came back through the anomaly and that Abby has been keeping him in secret. Abby begs him not to tell about this, and in exchange Connor convinces Abby to investigate the anomaly with him. He also convinces her not to tell anyone, so that they will have the glory for themselves and show Nick how useful they are.
At the same time, a workman goes along the affected London Underground tunnel with a big backpack sprayer full of insecticide, spraying about. A giant spider sneaks out and catches a rat behind him. The spider follows him for a time, before attacking him.
Back at the Home Office, James Peregrine Lester is growing increasingly sceptical of Cutter, but Claudia Brown defends him as their only expert and eventually convinces Lester to keep him involved ... for now. Lester also makes the very astute observation about Claudia's interest in Nick Cutter and warns her against having ulterior motives like romance for keeping Cutter on-board.
In his office, Nick, Claudia and Stephen Hart are going through Helen Cutter's files despite having gone through them years ago. Nick says that he feels guilty about his wife Helen disappearing, because Helen went to investigate an possible anomaly without him because of an argument between them about whether anomalies like this had had an effect on biological evolution. Interestingly enough, he decides not to mention the ammonite incident in Episode One or that he saw Helen; he keeps that information to himself.
Abby and Connor go to the New Forest to investigate the anomaly. They eventually get talking and Connor learns, to his dismay, that Abby is more interested in Stephen than him. He says that Stephen has no relationships with women and may be gay. Unknown to him, Abby then telephones Nick and tells him where they are.
In the dark beside a lake, Connor has fallen asleep when he should be on guard duty. Then what looks like an Allosaurus-like creature rears and roars, but it is an animated fake model and its two operators (Connor's so called friends who arranged the whole thing) run away as a Stephen and Nick arrive with swarm of government agents, assuming they were saving Abby and Connor from mortal danger. When they discover it was all a time-wasting hoax, at the worst possible time, Nick furiously removes Connor from the team. Abby tries to take her share of the blame, but Nick says she still has skills useful to the team. A despondent Connor is led away.
In a hospital, the bitten workman is examined. The doctor explains to Cutter and Claudia he has suffered a single wound to the neck, but the injury is not what is killing him: he is dying from poison (specifically venom). Cutter looks at the wond and concludes the wound is like a sting or bite, but is much too big for any native insect or spider. The doctor also mentions that the man was babbling about monsters when he was found.
Back at the Home Office Lester decides to close off the affected part of the London Underground (despite protesting how he is to tell the Mayor of London they must close the Underground because 'a fare-dodging creepy-crawlie is on the loose!') and send a team of men to investigate. Captain Tom Ryan and his Special forces team, armed with M4 and G-36 rifles and night-vision goggles go into the affected tunnel. Nick and Stephen want to go in with them but are not allowed to.
Ryan and his team find an abandoned room with a colony of giant spiders inside. The spiders, disturbed by the men and defending their offspring, drop on the men and try to bite them. In the ensuring battle the men find that their guns are malfunctioning: the gunshots are too bright and give off sparks. A spider falls on one man's neck, managing to bite him before another soldier knocks it off him. Ryan calls a retreat. On the surface, Ryan reports what he saw and tells them that the rifle fire had made sparks, along with his own physical sickness. Stephen concludes that these are signs of an elevated oxygen level in the air, as if a different atmosphere was coming through the anomaly. Nick deduces that the anomaly is not linked to the Permian like the last one but to the Upper Carboniferous. Claudia then informs them that the bitten workman has died and that they need to run tests on their own casualty.
Nick and Stephen are allowed down. Abby goes too after lying about her experience with spiders. Using what they learned from Ryan and his men, they are armed with bright torches and, as expected, the giant spiders retreat before their light. They go through a torn hole in some metal netting. They discover the anomaly in a corner of the room, and when they are investigating it, Abby sees two big long trailing arthropod appendages disappear round a corner. The creature- some manner of giant centipede- bursts out from its hiding place and attacks. In the mêlée, Abby and Stephen flee to the surface, and Nick gets driven deeper into the tunnels by the centipede which blocks the exit.
On the surface, Claudia tells them that Nick is in a tunnel which is blocked at its far end. Stephen and Abby mention the giant centipede, but admit they have no idea of its behaviour or how to contain it. Stephen suggest that Connor might know what the creature is and Claudia sends men to fetch him. Stephen, making use of the distraction, goes back into the tunnel alone to look for Nick. In the tunnels, Stephen finds a brazing torch and uses it as a rudimentary flamethrower. Its flame drives the giant centipede back and Stephen continues onward. However, when he passes the anomaly, its magnetic field sucks away the brazing torch. The centipede attacks again and Stephen is bitten. As Stephen lies on the tunnel floor, poisoned and delirious, a female figure enters the room through the anomaly. Stephen begs her for help, but she remains unmoving. Stephen looks the woman in the face, recognizing her as Helen Cutter.
Back in the tunnel Cutter finds Stephen still alive but delirious, and supports him on a shoulder as they go to safety. Stephen says "Helen will be waiting on the other side of the anomaly if he wants to know the truth."' On the surface Connor is discussing what the creature is: Arthropleura is suggested. Nick and the team arrive with the injured Stephen, and Nick confrims the centipede is what killed the workman, not the spiders.
When being taken to hospital, Stephen invites Abby out to dinner, remarking 'how much easier these things become when you're dying!'. The hospital staff inform Abby that unless they find a sample of the venom, so they can test it and see if it has any modern day equivalents, they cannot produce an anti-venom and Stephen will die. Nick tells the others that the Arthropleura must be caught before it can go back through the anomaly in order to get a sample of its venom. Cutter then offers to be the bait to catch it and tells Connor to find something to collect the venom.
Ryan and his men run up the tunnel using their torches to herd the spiders together and force them back through the anomaly. But the Arthropleura is nowhere to be seen. Though they initially assume it has retreated through the anomaly, Connor alerts them that Arthropleura were burrowers and it could have burrowed out of the room. The team then discover that it has burrowed a vertical hole in the wall and escaped.
Ryan, Nick, and Connor go along the narrow tunnel to a disused machinery room. The Arthropleura is on a rafter watching them. It comes down and attacks Nick; as it bites, he pushes forward against its mouth so that its fangs close encircling his waist and inject venom into two absorbent pads which he had under his suit. When it lets go, Ryan starts shooting at it, but the enraged Arthropleura rears about, knocking the gun from his hand. As Ryan scrambles for his gun, Connor begins hitting it with a metal stool. The enraged and wounded Arthropleura grasps the stool and rips it from his hands, but in doing so hits an electrical circuit box and receives a powerful electric shock to its head; it goes into convulsions and falls off the rafters to its death.
In the hospital, Stephen recovers slowly but seems to have amnesia, remembering nothing about Helen or asking Abby out on a date. Back in the underground, Cutter is watching the anomaly while they wait for it to close. He tells Connor that he will give him one last chance ... but not a cool nickname. He then feels the anomaly before it closes, thinking about his wife, but does not go through it.