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According to the recent episode "Fragments" he was first recruited by Torchwood in the late 19th century (1890s?) after being interrogated by Torchwood about his various references to "The Doctor" in converstaions and about his immortality.

These events must have occurred just after his return to earth form Satelliet 5. he apprently tried to get back to the early 21st century, but overshot the time period by over 100 years. So he had to wait all that time to find a version of the Doctor that coincided with himself.