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The Clone Doctor was created as a result of regenerative energies present within The Doctor's severed hand.
When Donna Noble touched the casing of the severed Hand, it broke as it took in the Human DNA and created a Time Lord/Human hybrid that possessed one heart and aged as a Human did. The clone also contained parts of Donna's personality and mannerisms but mixed with his own intelligence.
The clone stays with Rose Tyler and Jackie Tyler in Pete's World. (DW: Journey's End)
