Back at the ship, Darwin awakens. He takes his fellow team members outside and cares for them with his medical training. When Havok regains consciousness, he searches the ship for any sign of Nocturne, but cannot find her. While searching the pod bay, he discovers a bio-bomb, designed to destroy all living organisms in a two-mile radius. With the help of the team he manages to deactivate it, but at the cost of depleting his entire energy store. Havok, team leader, was now down. After days of scouting the outskirts of Cardiff, the team decides to elect a new leader. Darwin is chosen unanimously.
Meanwhile at the Institute, Nocturne’s threats become more serious. She continues to demand information. The Doctor decides to tell her everything about the ship crashing, only finding her and taking her here. At first Nocturne does not believe him, but she reads his memories and realizes he is right. The Doctor reconciles with her, thinking that not only is she an alien, but the last of her species. Eventually she agrees to relinquish Amy, if the Doctor takes her to the crash site. They go to the crash site, but Nocturne accuses the Doctor of lying, as there is nothing there. Torchwood starts a national search for the ship and its inhabitants, while the Doctor takes Nocturne to the TARDIS to see if the ship shows on the console. After confirming that everyone in the TARDIS is asleep, he lands it in the Library, a place he had been to previously and where he first met River Song. He searches for hours in encyclopaedias and compendiums, but cannot find any reference to Nocturne. After almost giving up, he finds a book entitled Mutants: The New Evolution. At that same time the TARDIS malfunctions, causing the Doctor to rush back. He guides Amy through the steps of fixing the problem at the console. Before he can finish, an old enemy appears…
The team decide to look for Nocturne in the city, using the tracking skills of Black Death, he follows her scent to the Institute. They formulate a plan to get inside. Black Death generates a disguise for them all, and they eventually find the room where Nocturne was kept. Before they can go inside, Gwen Cooper sees through their disguise with the training she received against psychic abilities. She attempts to take them in, but they retaliate, causing a battle to ensue between the mutants and Torchwood. The team wins and easily levels the building with their mutagenic abilities. Torchwood declares to the public that the destruction was a natural disaster and that the rebuilding of the Institute was already underway. The team unified with Torchwood, realizing that both could help the other. Torchwood withheld the information that Nocturne was in fact alive, as the team assumed she had died when the building was destroyed. Torchwood knew that the team would leave if they knew she was alive. They named the new alliance the Vortex Guardians.
At the Library, the Doctor was being chased by the Vashta Nerada, the shadows that melt the flesh. He navigated himself around the library with his sonic screwdriver. He ended up in the atrium, with shadows at all sides. He knew he could not survive much longer. Suddenly the TARDIS appeared, homing in on his signal. He escaped the library with the book. After studying it, he knew; Nocturne was a mutant.