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Rupesh Patanjali was a doctor, originally from the Midlands, who worked at the A&E department at St Helen's Hospital in Cardiff. Jack Harkness and Ianto Jones encountered him while they removed an alien Hitchhiker from within a patient. His interest in Torchwood piqued, Rupesh tracked them down to the Bay and Gwen talked with him at length. Soon after, he assisted the Torchwood team in helping several children caught in the thrall of the 456. He seemed well on his way to becoming Torchwood's new doctor, replacing the late Owen Harper.
However, all was not as it seemed. After luring Harkness back to the hospital with a report of another Hitchhiker discovery, he unexpectedly shot Jack in the back, "killing" him. Patanjali was working for the UK government, and was originally to have been planted within Torchwood 3 as an MI5 infiltrator, to get information on Torchwood from the inside. Instead, he was ordered to incapacitate Harkness by another agent, Johnson. He also killed a patient in order to facilitate the ruse of getting Harkness back to the hospital, which resulted in Johnson rebuking Patanjali when the doctor expressed discomfort over the apparent death of Harkness.
Jack was subsequently "re-killed" several times as Johnson's team implanted a bomb. Patanjali asked Johnson what was to become of him, now that his cover had been blown. Her silence indicated that, in order for the mission to succeed, he must also die. Fearing for his life, Patanjali tried to run away, but was shot in the back by the cold-blooded Johnson. (TW: Children of Earth: Day One)
His body was then taken to an MI5 compound. When Gwen Cooper and Rhys Williams went to rescue Harkness from the same compound, they found his body. (TW: Children of Earth: Day Two)
It's uncertain whether the Torchwood team ever discovered the truth about Patanjali's murder, given that they later work alongside his killer, Johnson.