@omegablast452: He's not part of the TARDIS, gotta point that out. He is linked to it telepathically, but not physically part of it. He gets captured because he doesn't attempt to game reality. Also, he was captured by the Master, someone who has insane luck/plot shields in the show as well, so they might just cancel each other out :P
He used a gun in that scene because he was getting the entire group away, not just himself. He was blowing up the artificial gravity generator.