The Doctor responds to a Time Lord distress signal and follows it right out of the universe, directly to another one of those planetoids possessed by a disembodied spirit. Hate it when that happens. When they arrive, the Tardis goes dead. Again, hate it when that happens. Anyway, on this planetoid they find a couple of dirty cockney servants, an Ood, and Helena Bonham Carter. Said madwoman kisses and then bites the Doctor before being locked away for everyone's safety. The Doctor thinks he hears the thoughts of a bunch of Time Lords, but it's not long before he realizes that what he's really hearing are a collection of distress calls, all of whom had been lured out of the universe and killed. He also realizes that the dirty cockney servants are ragamuffin creatures put together by the disembodied spirit out of the bodies of various beings. And finally he realizes that Helena Bonham Carter is actually the physical embodiment of the soul of the Tardis. Unfortunately, he doesn't realize that until after the disembodied spirit possesses the actual Tardis and leaves the planetoid, taking Amy and Rory along.
This leads to a nice sequence in which the Doctor and HBC try to reconstruct a Tardis out of the remnants of the Tardises that had come along with all the other Time Lords previously killed on the planetoid. While the Doctor and HBC are carrying on like a married couple, the actual married couple are being toyed with like rats in a maze aboard the Tardis. Once again, Rory dies, but this time it's a purely hallucinatory death. The Doctor does eventually create his improvised Tardis, and flies it after the actual Tardis, while HBC sends a telepathic message to Rory ("the pretty one") giving him the information he and Amy will need to drop the force field so the Doctor and HBC can come aboard. In the end, the Doctor tricks the disembodied spirit into transporting the entire crew to the main control room, where the soul of the Tardis abandons the body of HBC and takes control of the ship back from the disembodied spirit. And then the Doctor has a very romantic goodbye scene with his one true love.