Dear Diary,

The Doctor and I have been travelling together for, oh, maybe a few months now. He went off on his own, shortly after our excursion to Venice, allowing me and Rory to, well, do what all Honeymooning couples must eventually do. Although he was never very willing before, Rory seems even less inclined than ever – probably thanks to having met the Doctor in the flesh – to take part in my little role-play sessions. Oh, well. I didn't tell him about what happened between me and the Doctor just before our wedding day – of course I bloody didn't, I'm not completely stupid! – and he already feels jealous enough knowing about my crush on him. Fourteen years and five months later, and I'm still calling it a crush? It doesn't feel like anything more, anyway.

No wonder the Doctor finds relationships baffling; if we can't even work out how we feel about each other at the best of times, how can an alien time-traveller who has to deal with the fact that he may or may not already have a wife that he doesn't know all that well? That River Song was an interesting character: the way she interacts with the Doctor – flirting with him one one minute, needling his perceived pomposity the next – is totally at odds with the way everyone else who meets him behaves. Most people are totally in awe of his intelligence, or just too dazzled by the stream of babble to really notice anything else about him. River treats him as though … well, he's human, not some 'Complex Space-Time Event', I think his words were.

The thing about the Doctor – the thing I find most endearing about him, anyway – is his sense of fun. Even when our adventures take a turn for the worse, he still manages to make you feel as though everything is going to be all right. Nine times out of ten, he's right, of course. If things go bad, he'll sulk about his perceived failure, but he never dwells unduly; I suppose it's a defence mechanism, more than anything: he'd never have time for anything else if all he did was worry about the mistakes of his past. There's this 'Time War' that he mentioned once or twice, but he won't go into details. I gather that he lost his whole family, though; if we was as close to them as I was to my parents, I can see why he doesn't talk about it much. Some things, you just can't.

For instance, something has been plaguing the Doctor since he came back for me. From my perspective, he was gone for about a week; for him, however, it could have been years. He didn't look much different, but he was curiously muted; he never spoke about the places, or times, he had visited, never rattled off a list of famous names he had encountered, and he never even sprouted a stream of confusing tech-talk about the TARDIS which was the biggest give away that something was troubling him. I did ask if everything was okay, but as was typical with alpha-males across the breadth of the universe, he brushed it off. What is it with men – even aliens – that they can't talk about their feelings?

After that, though, it seemed like just another typical day in the TARDIS: the Doctor standing proudly at the console – I'd noticed that he'd deliberately locked the parking brake in order to ensure that the ear-grinding noise would occur whenever we landed – looking over a list of planets that were in the immediate vicinity and trying to decide which one to go to next. "There's [unpronounceable name]. It has a wading pool of liquid amber, very relaxing. There's [sounds like 'Ham and Cheese Six'], famed for being the first planet to build the space elevator. Of course, I had to give them a hand, as they only have the one." It was easy to spot just how forced his levity was; there was a darkness to him that I'd never seen before, but he was trying not to let it ruin my return.

Things kind of came to a head a few days later; interestingly enough, it had been just after another meeting with River. Throughout the whole adventure, the Doctor had been oddly disaffected and almost entirely distant: a very big change from the usual repartee they shared. Once we were back safely in the TARDIS on our way to River's home world, she had snuck up behind him in order to give him a hug. The Doctor acted like had just been slapped or something; he pushed her – quite violently, too – away, yelling at her to NEVER do that again, and then, tears in his eyes, he disappeared into the TARDIS' innards for the rest of the trip. Me and River looked at each other for a long, uncomfortable moment, wondering one or the other of us ought to go and find him. The fact that, even though River knew the Doctor better than he knew himself at this point, she had no idea what was the cause of this behaviour was … troubling.

From that point on, the Doctor became increasingly insular, preferring to spend the time between planets fixing the million-and-one things he claimed to be wrong with the TARDIS; whenever I tried to speak with him, he would either respond with one word, or not even respond at all (it's difficult to decide which was worse). I figured that some 'positive reinforcement' might help to draw him out of his shell, but whenever I tried to pay him a compliment, it would backfire … drastically. He would react as though you had said the most insulting thing possible, mope around the TARDIS for hours on end, before returning to the console room and pretending nothing had happened. Whenever someone would show a personal interest in him, he'd look like he was about to be sick, rather than just being cutely naïve about it as he had been with me back in my bedroom.

I'd noticed that he'd started wearing a big, brown overcoat that almost wrapped around his lanky body twice; even though it was was natty and torn, he refused to take it off. Even when the planets we were on had three suns and the sweat was sticking his clothes to him, he'd just shrug and say that he was fine. I honestly can't tell you much it hurts when someone you care about won't speak to you; even though you know something inside is killing them, they worry that you'll think less of them … they're worried about leaving themselves vulnerable, exposed to attack. In a way, though, it also made me stop seeing the alien. The Doctor might have been weird and wacky and wonderful, but at his core, he was more human than the rest of us combined.

Finally, it got to the point where I was seriously frustrated with his behaviour and could no longer stand his evasiveness; it was poisoning what had previously been quite a fun relationship, and so, I strode angrily into the console room one morning – or afternoon, or night, it was impossible to tell – and told the Doctor in no uncertain terms that I wanted him to take me back home to Rory. For just a moment, it looked as though he was going to offer some kind of protest, but he said nothing, merely busying himself with adjusting the coordinates. It took only a matter of seconds for the loud thump that indicated arrival to echo out of the console. "And we're there," the Doctor added unnecessarily. "Leadworth: hardly the most stimulating spot in the universe, but nonetheless, some like to call it home." He was almost like his old self.

"Well," I said, not quite knowing how to finish that sentence off. The Doctor was saying nothing; he was rooted to the spot like a Weeping Angel under scrutiny, absolutely immobile. I was starting to wonder if Time Lords had some kind of inbuilt feature that stopped them from saying what was on their mind. He just kept looking at me, as if he was wondering what was taking me so long to leave, wondering whether he ought to point in the direction of the doors. I sighed, quite loudly and theatrically, and slammed my fist down on the console in the most childish gesture I could muster. "Are you really just gonna let me walk outta here without telling me what's wrong?" I was so angry with him right now, for putting me in this situation, that I wished I could slap some sense into him.

I have to tell you, it was one of the most heartbreaking things I've ever seen when the Doctor flopped down onto the floor, an expression of utter defeat on his face. You have to understand, the Doctor's always so full of energy, so full of life, and he never, ever gives up … so to see him like that, slumped on glass dais hanging over the heart of the TARDIS, was incredibly difficult. His dark hair was covering his eyes, but I could see the wetness dripping down his cheeks. I moved to his side and tried to put my arms around him, but he shrugged me off – just as he had with River Song – as if physical touch was a harmful, repulsive thing to be avoided at all costs. "Please, just don't touch me!" he said weakly. I sat next to him, tried to look into his dark eyes, but they were glazed and unfocused.

"Something happened while I was travelling," he finally said after a long eternity of silence. "Things always happen to me – even if I don't necessarily invite them – as you've seen for yourself, but this was different." He paused to take a deep breath, steeling himself for what was to follow. I wanted to reach out, to offer what small comfort I could, but he backed off, not wanting intimacy, emotional or physical. "I thought the Time War, losing my friends and family – indeed, my whole world – was the worst thing that could happen to me." A small, bitter chuckle escaped his lips. "It doesn't happen very often, but I was proved very, very wrong. There are much worse things than losing everything. Even when everything has been taken from you, you can still lose yourself. And that is greatest loss of all."

I wanted to say that I understood, but I didn't. I couldn't be sure whether or not this was some weird, Time Lord thing that I could never hope to comprehend. Had he lost something, some part of himself, that he couldn't regain, or was it – in human terms – something that had left him with a sense of violation, so he no longer felt comfortable in his own skin? "Doctor, whatever it is, you can tell me. I'm your friend, I want to help. If there's something I can do to help you get back whatever it is you've lost, I'll do it." The words felt small and pathetic, but I didn't know what else to say; I didn't want to bombard my friend with a lot of hopeless, helpless clichés that would just leave him feeling more annoyed and distant.

The Doctor took several deep breaths at this point, probably to quell the rising sense of panic he was feeling at recounting what had happened. "I went to the Millennium celebrations on Alpha Verzamel; it's one of my favourite planets, and I had a standing invite to attend the festivities. I thought that, since I was on friendly terms with most of the populace after having done them a favour a few regenerations back, I'd be all right. Not so. At the party, there were a couple of women who were, ah, a bit keen, I believe is the phrase. I politely told them no and thought no more of it. I don't know if they attacked me or slipped something in one of my drinks, but as I was making my way back to the TARDIS after the party, I passed out."

I felt a sudden knot of horror in my stomach; I wanted the Doctor to end the story there, as I knew what was coming next. He must've saw the expression on my face as he managed a small, pitying smile. A laughed a tremulous, derisive snort. "See, Amy. It isn't all Weeping Angels, Daleks and giant eyeball ships. Even the big, bad Time Lord can be a victim of people who just won't accept no for an answer." The Doctor shivered and pulled his overcoat around himself tighter, trying to form a protective cocoon between himself and the environment. There was so much I wanted to say, wanted to do, not least of which was to find the spiteful bitches responsible for this atrocity and tear them apart with my bear hands.

"Did, uh, did you inform the local authorities of what happened?" I asked, feeling cold and numb; torn between my quaking rage, and my need to try and offer comfort – no matter how small – to my friend, I was scratching the back of my hand with my nails in an attempt to feel something. No wonder he had been so distant lately; River's surprise hug must've made him feel like he was being jumped again, and my attempts to compliment him would've felt like he was being made to relive that day over and over. A small, dark part of me really hoped that Alpha Verzamel had a death penalty and that these loathsome creatures had been made to suffer for the terrible crime that they had committed.

"No," the Doctor said, standing up. "Really, what could be done in that situation? They would've claimed that I'd at least have given tacit consent in my inebriated state, and no matter where you go in the universe, the word of the fairer sex is always going to be given more weight." I watched him fiddle with some of the controls; more than likely, he was just looking for something to do to avoid talking to me for a bit. For my part, I wasn't sure what to say. I wanted to order him to take me to the planet so I could deliver my own brand of justice, but somehow, I suspect that – in his infinite compassion for all things – he would take issue with that plan. That the Doctor could see the value in even the lowest scum in the universe was both his greatest strength and biggest weakness.

I'm sorry to say this, but there's no easy resolution here. I wish I could tell you that, after a couple of weeks, the Doctor was back to his hunky-dory self, but life doesn't work that way. Eventually, with a bit of work, he got over his aversion to physical contact, but even now, I can still see the tiny pool of darkness behind his eyes. Fear. Something I'd never seen him display before. He's been hurt, badly, and I'm honestly not sure he'll ever truly recover from it. For now, though: I stay by his side closer than ever, and I watch out for him with constant vigilance. I will never, ever let anything like this happen to him again. Not to my Doctor.