The Doctor would likely have to be unconscious in the corner for this to happen, so Jamie would be worried. And as he was never really allowed to touch the controls, (he can read the displays and open the door, and that's about it) he'd flail about for a bit trying to figure out how to actually fly the TARDIS. (He does know in general where the part is to control the flight, though, so it wouldn't be that long.)

Once he figured it out, he'd try and take the Doctor somewhere like the Wheel or someplace he's been that he knows has good medical technology. Of course, they'd wind up somewhere completely different, because if Two can't get them to where he wants to go, the chances of Jamie actually doing that are about nil. :)