By 2009, Rupesh had been working with the British government for months to infiltrate Torchwood Three. Rupesh first encountered Jack Harkness and Ianto Jones when they removed an alien hitchhiker from a deceased patient. Realising they were Torchwood, Rupesh tried attracting their attention with a series of bodies that had been vanishing from the mortuary. Ianto and Jack declined. Rupesh tracked them to the Bay, where another Torchwood member, Gwen Cooper, talked with him at length about Torchwood Three.
When the children of Earth began saying "We are coming" in unison, his initial orders had changed. After luring Harkness back to the hospital by killing a patient matching the profiles of the other disappearances, he shot Jack in the back, killing him.
Johnson's team implanted a bomb inside Jack before he resurrected. 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. (TV: Children of Earth: Day One)
His body was then taken to Ashton Down and his family requested its release. When Gwen and Rhys Williams went to rescue Harkness from the same compound, they found his body. (TV: Children of Earth: Day Two)