Well, yes - he *was* exterminated in the TVM (right at the beginning!), before tricking the Doctor into transporting his remains, escaping (in the form of a snake-like 'essance'), and taking over the body of a poor paramedic....before finally attmepting to steal the rest of the Doctor's lives
Although he was defeated and 'destroyed' by the Doctor at the end of the TVM, he was then ressurected by the Time Lords, to help them during the Time War against the Daleks.
Seeing the carnage, he then chose to run away, disguise himself as a human, and alter his memories, so his identity became a secret, even to himself.
As to the Martha/Freema Agyman question, she WILL return for the second half of next years' series (although she's going to be in three episodes of Torchwood first....oh yes...Lesbian clinch for Martha, anyone?

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