Originally Posted by Kody
No, I can't come up with a better explanation for his death off the top of my head. But I wouldn't have needed to think of one because I'd never write such a crap story. 
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He could have said it had something to do with that huon energy crap from The Runaway Bride. The Doctor could have been accidentally dosed with residual huon energy that escaped when the underground base was destroyed or something and it inhibited the regenerative process, when in the actual timeline the Doctor made it out in time and thus the energy release was harmless and it merely dispersed. After all, the Doctor did say in The Runaway Bride that the Time Lords supposedly removed huon energy from existence... inhibition of the regenerative process would be a pretty damn good reason for them to do so, considering they're not really supposed to get involved in most things.