The Doctor had infact passed out from pain. He was breathing deeply , He seemed to be trying to recover somewhat as well. He was unaware of what was going on. He stayed unconnious. The TARDIS could see Seclusion has no idea what to do , the ship started itself up. Anytime anything went wrong she would do that. The TARDIS was off with no warning either. 
The TARDIS picked Torchwood Cardiff, just as she was off something went wrong, causing her to loose control. The Master had done something soon as he got free.

Though the TARDIS was able to get to Cardiff she crashed landed and seemed a bit damaged, The Doctor awoke groaning and was looking around. He seemed panicked seeing they had crashed.
He checked over the TARDIS and goes to see if Selcusion is ok too. He winced from pain "Are you ok?"