6. Reset

Jack recruits UNIT medical specialist Martha Jones to assist Torchwood after a series of deaths of drug trial subjects from the secure medical facility called the Pharm, which Martha, and Torchwood's medic Owen, identify as murders. Further investigation shows that the murder victims have previously suffered from incurable diseases such as diabetes and HIV, but were cured of them prior to their deaths. One victim, Marie, still alive when Torchwood find her, dies while being questioned and fly-like creatures erupt from her mouth.

Jack detects a strong presence of alien life forms within the Pharm, and the facility's security system proves to be beyond the ability of Torchwood to hack from the outside. Martha offers to infiltrate the facility disguised as a human test subject and is accepted after claiming to be infected with hepatitis. Once inside, Martha discovers that the Pharm uses a substance called Reset that releases alien parasites called Mayflies into the host's body. The parasites cure the patient of any diseases and restore them to "factory settings", but at the price of infecting the patient with the parasite. When the eggs hatch, the creatures destroy the host. The director, Professor Aaron Copley, injects Martha with multiple doses of Reset, curious to determine the effect of Mayflies on her immune system, which has changed from travelling in time.

Martha compromises the Pharm's computer systems. Torchwood discover Billy, the assassin employed by the Pharm to dispose of research subjects, and realise he is about to kill the last living test subject. Ianto and Gwen apprehend Billy and return him to the Hub for questioning. Billy is infected with Mayflies, likely contracted from one of his previous victims, and Owen kills him by improperly using the singularity scalpel. The team rush to the Pharm hidden in Billy's vehicle, using his corpse in the driver's seat to fool the security guards into letting them inside the compound.

Within the Pharm, they find numerous aliens being used to produce various test substances, including the mature Mayfly that is the source of Reset. Owen successfully uses the singularity scalpel to neutralise the Mayfly within Martha. Jack orders Toshiko to shut down the Pharm, euthanising all of the trapped aliens with inert gases, and crashing all computer systems. Before the team depart, Copley kills Owen by shooting him in the chest and Jack responds by shooting and killing Copley.