SPOILERS BEHIND THE CUTS!
While in mid-flight, there is a knocking from outside The TARDIS. This confuses The Doctor as there shouldn't be any way that anything should be able to come in contact with The TARDIS while it is traveling... except for another TARDIS or something created by a Time Lord.
Cue the entrance of a strange little cube, exactly like the one that The Doctor once used to send an emergency message to the Time Lords (As seen in the 2nd Doctor story The War Games!) It turns out the message is from The Corsair - a Time Lord and old friend of The Doctor's - and that it was sent from a pocket universe outside the normal flow of space and time. Excited by the prospect of another Time Lord being alive, The Doctor charges forth, jettisoning spare rooms from the TARDIS to get the extra push needed to dimension jump.
Upon landing, The TARDIS console suddenly powers down completely. Further investigation reveals this pocket dimension to be a giant scrap yard, populated only by two strange humanoids called Uncle and Aunt and an Ood Servant they call Nephew. There's also a madwoman named Idris, who kisses and assaults The Doctor, saying many confusing things. And the whole place is ruled over by a sentient force called House. All of which is fascinating to The Doctor but not nearly as pressing as the issue as where The Corsair is... or the dozens of other Time Lords he swears he can hear the voices of in the air around him.
It is only when The Doctor finds a chest full of message cubes that the answer becomes clear... and only then that he notices that the scrap around him is made primarily of TARDIS parts. House takes possession of the now-empty TARDIS, while Amy and Rory are still inside it, and makes a break for the other universe... leaving The Doctor trapped on the quickly cooling asteroid with the woman Idris, who is now housing the soul of The TARDIS!
THE GOOD PARTS
1. All The Questions We Get Answered!
It's amazing how many long-debated questions Neil Gaiman answers so matter-of-factly in this episode. For instance, Wholigans have long debated whether or not it is possible for a Time Lord to become a Time Lady or vice versa - that is to say if regeneration can cross gender lines and if there is a chance that - someday - we might have a female Doctor. With an off-hand remark about The Corsair being a nice man - and a nice lady a few times - The Doctor confirmed that there's a chance he could become a she. Someday.
There's also been a suggestion among the The Fandom that The TARDIS - which we've known to be independently intelligent to some degree since the third First Doctor story Edge of Destruction - was taking The Doctor who where he needed to go to help people, thus explaining away why The Doctor always seems to find trouble no matter where he goes.
2. All The Questions We DON'T Get Answered!
The idea of The TARDIS (or indeed, all TARDISes) having souls has been a part of the show mythology for sometime - and for all that this episode does to explore the concept, we get surprisingly little explanation for just... how? How does a machine develop a soul? Are Time Lords themselves placed into the machinery? Answers are not forthcoming... nor should they be. Doctor Who works best when there are still mysteries to explore and The Doctor (and his technology) should be a part of that mystery as well.
3. Running Up And Down The Same Corridor Over And Over
The bits with Amy and Rory trapped inside the TARDIS halls are very effective - both for the horror involved - and as a neat twist on the cliche that all Doctor Who stories that do not feature a bunch of people running around a rock quarry consist of endless scenes of people running up and down the same corridor over and over.
4. No Annoying Amy/Rory "Do They Really Love Me?" Sub-Plot
Well, okay... there is a bit where Amy stumbles across the body of an apparently dead Rory, who took the time as he was going mad from loneliness to scrawl several thousand variants of "I HATE AMY! DIE POND!" over and over on the walls of a hallway in his own blood. But that doesn't count and it's a neat way to illustrate how much Amy is in love with Rory... that the fear of being hated by him is such a crippling thing to her.
5. The Doctor and His "Wife"
Really, the whole conceit of The Doctor and The TARDIS finally getting a chance to talk... really talk... is a brilliant one. And the Interplay between Matt Smith and Suranne Jones is perfectly executed.
1. Why So Surprised, Doctor?
Granting that the exact circumstances are different, The Doctor probably shouldn't be as surprised as he is by The TARDIS being depowered after leaving The Universe. After all, the same thing happened in the Second Series episode Rise Of The Cybermen.
2. Not To Be That Guy, But...
... as original and wonderful as the idea of The Doctor and The TARDIS being able to communicate directly is, I'm afraid it's been done before and done recently. And irony of ironies, it was in the Doctor Who comics.
Doctor Who: The Forgotten has an Amnesiac Doctor being guided out of a trap by the soul of The TARDIS, who manifests itself as various ex-companions of The Doctor as needed. The two are able to communicate for quite a while, with The TARDIS calling itself The Doctor's first and oldest companion and - in one touching scene - manifesting it's soul as Susan, The Doctor's Granddaughter, so that he could - in some fashion - say goodbye to her.
I don't think Neil Gaiman read the comic in question before hand and I'm not accusing him of plagiarism. I just had to note this before all the other Wholigans start singing about how original the conceit of this episode was and give a shout out to one of the best Doctor Who comics in recent memory.
The Final Verdict: Hopes were high going into this Neil Gaiman penned episode and he did not disappoint. The mythology of the show is referenced and enhanced, but we're left with more questions than we are given answers. And that is all too right. A well-paced script is backed by some excellent performances, leaving us with the best episode of the Series thus far.