This was rather obvious this one, I mean come on, even the RTD era kept banging on about this, the TARDIS is alive, so all those bangs, sparks, explosions, etc, would cause a bit of pain, but as The Eleventh Hour shows, the TARDIS can also heal itself, and again, as with The Eleventh Hour it can also fully change itself to.
Now, in CotBS, the poor thing is confused already as it's following a distress signal but somehow ended up on a Pirate Ship. Which was explained with the whoel two plains thing, etc, etc.
Doctor and Captain mess around, TARDIS starts to spark off, in pain, Siren comes after it, TARDIS finally figures out it's in the wrong place (Doctor Doesn't) and it goes to the other ship instead.