This story is a sequel to Doctor Whooves and the Auton Invasion of Equestria

Doctor Whooves 1.2
Written as part of my Doctor Whooves series. Can be read on its own, at a pinch.
A story of love, and of friendship. A story of growing up, of growing old. Read it. Read it now. If that hasn't captured your interest, here's a message from the Doctor himself:

"Attention, readers! This is the Doctor speaking. I'm in a spot of bother. Having foiled an invasion attempt by the Autons, I was just trying to relax for the first time in about a century when someting else cropped up. It seems that another pony in this town has been going around for years pretending to be me. I am not best pleased at this. Who he is and why he's doing it I don't know... yet. It looks as though it's down to me to solve this little problem myself. Typical. And to think that the Timelords sent me here to keep me out of trouble. Chance would be a fine thing. All I know so far is that he's friends with the local mailmare, so all I have to do is track her down and talk to her. That should be no problem at all. Although oddly, some of the ponies in this town are remarkably difficult to talk to. Miss Sparkle seems to think it's my fault in some way. How she ever became a princess I'll never know."

Note: as before, this story takes place during the season 5 hiatus.
The Galgonquans, one of my favourite alien races, are taken from Aliens in the Family, a charming book my Margaret Mahy, later adapted into a TV series for the BBC. I have taken shameless liberties with the background of their species. I'm like that.

Doctor Whooves 1.1
Something is happening in the skies of Ponyville. Something that has been waiting a long time to return is about to make its move. This time, it's not just world domination it has in mind. There could be a chance of some revenge as well...
The Doctor is old. So old that he's begun to make mistakes, and, being who he is, these mistakes are usually not of the 'oh dear, where did I leave my keys?' sort, but more often of the 'press this button and the Cyberponies' spaceship will be eradicated... oh dear, I've destroyed the planet' sort. This sort of incompetance hasn't gone down very well with the High Council of Time Lords, who have exiled him to his favourite place: Equestria. Unfortunately, they've picked a time a few decades after the one he's used to.
Recovering, in the care of the kindly Fluttershy, from the regeneration through which the Time Lords forced him, the Doctor discovers that an old enemy has come back to haunt him. The Nestene Intelligence has returned to Equestria once more. He is determined, however, to defeat it by enlisting the help of the legendary Bearers of the Elements of Harmony. There are only two small but daunting problems with this proposal:
1. He can't walk in a straight line without falling over;
2. Everypony is convinced he's a lunatic, and is going to take a fair bit of unconvincing.
Meanwhile, Princess Luna, with the help of Professor Crater Mass, her scientific advisor, is making her own enquiries, but what are her true motives? As the death toll mounts, the Doctor begins to realise that he may be out of his depth.

Set during the season 5 hiatus, for some reason.
My first story, already a mess of elipses and clichés. For anyone who's interested, the Doctor involved is the 22nd, so your 'headcanon' should already be in tatters. Read this anyway. Read it and like it. You know you ought to. I'll try and make it fit with MLP's canon, anyway. I thought that since the Autons have already been used to introduce two great Doctors, why not make it three?
This is not a 'Doctor travels into the Ponyverse' type crossover, more just a 'The Doctor, who is already there, bumbles into our favourite characters for the first time' sort of thing. It's loosely based on the TV story 'Spearhead from Space', but it's not a retelling. I did say 'loosely'. The title will only seem anything other than ridiculous if you're familiar with the Target novelisations, which I'd imagine roughly none of you are. Ah, well...
Rated teen for violence, but nothing gory. Nothing you wouldn't see in Doctor Who, in fact. If you've read this far, you probably ought to read the story.
For listening, some saint has uploaded a Spearhead from Space suite, which I heartily recommend to any Doc 'True nuts out there: https://www.youtube.com/watch?v=Dx7-oCOOX_I