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Yvonne Hartman (the Torchwood leader) was simply strong willed enough to retain her identity, including her powerful sense of duty to "Queen and Country". The Torchwood episode "Cyberwoman" and the Christmas special "The Next Doctor" both also indicate that individuals can retain some of their identity even after conversion (see also Oswin Oswald post-Dalek conversion in "Asylum of the Daleks").