S02E06: 'Reset'

Martha Jones, now working for UNIT in a senior medical capacity, turns up at Torchwood to help them examine a corpse. She notices that it has been pumped full of chemicals and the eyeballs have puncture marks at the bottom. Several attacks involving needle marks take place and Torchwood discover that the victims are all linked because they have had incurable diseases supposedly cured after visiting a clinic called The Pharm, run by Professor Copley.

A woman who survived an attack reveals that she was paid money to keep quiet after having her AIDS cured. However, she has a seizure and dies, with fly-like creatures emerging from her mouth and quickly dying when they cannot find a host body in time.

Martha Jones is sent in undercover to The Pharm for clinical trials, equipped with a hidden camera and claiming to have hepatitis. Meanwhile, Owen agrees to go on a date with Tosh.

At night, Martha sneaks into The Pharm's office and transmits computer files to the Hub. On the premises, a massive alien fly has broken out and the area is roaming with security, who find Martha and tranquilise her. When she wakes up, in restraints, Copley tells her that her blood is unique from travelling in time and space.

Martha has the alien larvae implanted into her stomach, but the Torchwood team break into The Pharm and demand that Copley remove them. He claims it is too late, but Owen uses a special alien device to extract the aliens from her stomach without breaking her skin or hurting her.

Jack declares his intention to destroy The Pharm, which contains various aliens used for experimentation purposes. Owen tries to reason with Copley, but he pulls out a gun and kills Owen. Jack retaliates by shooting Copley in the head.