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He is a in-between incarnation between the 8th and 9th or he could be the actual ninth Doctor making Eccleston the tenth. In other words, he's the doctor that fought in the Time War.
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Yeah, that was my thought. Seems too obvious, though. And while the Doctor isn't proud of what he did in the Time War, he's never really been so ashamed as to disassociate himself from it.
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I don't remembered the Doctor 'thwarting the intelligence at every oppurtunity', in fact I'm pretty sure I've only heard of it in one episode so I just wonder why he's such an influential and important antagonist.
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Twice in the last season and, if memory serves me correctly, twice in the original series run.