Author's Note:Not quite the end, but definitely getting close now :) This has definitely turned out longer than I had originally anticipated, but I've enjoyed writing it, and hope that you have enjoyed reading. Thanks as always to those of you who have read this far, and many thanks to those of you who have reviewed :)

38. Homecoming.

Amy blinked and opened her eyes blearily, her sleep-befuddled mind stuttering to a halt as it clambered out of the dream that it had been immersed in. She floundered for a moment, semi-conscious, trying to make sense out of the world. She was lying on something soft; she had fallen asleep in bed then, this time.

She splayed her limbs out like a starfish and turned her gaze to the ceiling, feeling her mind become more lucid with every passing moment. Something wasn't right. She searched her mind for the information, but simply found a crushing sense of hopelessness and loss. Had someone died? She slowly counted the cracks in the ceiling. There was the same number there had always been. They really needed to repaint.

She sighed. An echoing sigh to her left told her that Rory was still asleep. Amy glanced at the clock by the bed, having to squint slightly through eyes that did not want to cooperate. Either she needed glasses (never!) or she was still sleepier than she had thought.

05:00.

Humph. She immediately wanted to punch whatever had dared to wake her so early. She pricked her eyes, lying stock still, trying to work out what had made the noise. Yet the house was still. Odd. She had been sure that something was supposed…

And, just like that, reality came crashing over her like a tidal wave, multiplying her sense of helplessness and loss by leaps and bounds. The wave closed her eyes against her wishes, and she felt her heart flutter, her stomach leap, her entire body exuding panic. But surely that had just been a bad dream?

Ignoring the nagging thought telling her that this happened every morning and that she should really be used to it by now, Amy quietly got out of bed and padded over to the window. The curtains were open; both she and Rory had been too tired the night before to close them. She pressed her face right up against the glass, feeling the cold from the window pane seep through her skin and into her bones. There, in the middle of their garden, stood a tall, dark shape, much like it had all those years ago. Only it was standing upright this time.

The TARDIS looked exactly as it had when it had first arrived, though to Amy's mind it looked more mournful than ever, as though it were standing vigil. She could almost hear the whining noises that it would be making as it longed for the faithful Time Lord to return, to whisk it away in adventure. But he was never coming back, was he?

She sighed again, her breath fogging up the glass. Reaching up with a shaking hand, she wiped the mist away, her eyes focussing once more on the lonely box sitting on the grass. She blinked.

No. It couldn't be.

She glanced at Rory, hoping that he could provide her with some much-needed reassurance ("No, you're not going crazy, it's just a gnome. There's no one there."), but he was still asleep. Amy looked back out the window. She hoped Rory hadn't gone and bought gnomes again – the last novelty one had been so lifelike and large that she had, upon waking up in the middle of the night and looking out the window, run out to the garden, shrieking the Doctor's and River's names. And then found a bloody gnome, fishing rod in hand, stupid red hat sitting crooked on his head, smiling smugly at her. And then she had turned around to find Rory staring at her from the window, his face a picture of confusion. Once she had trailed sadly back into the house and told him what had happened, he had of course got rid of the gnome.

But there it was again. Except there were three. And they were moving.

Amy tiptoed backwards, eyes fixed on the window, scared to make any noise, and poked Rory soundly in the ear.

Rory awoke with a startled and pained snort. "Ow!" He swatted at his ear. "Mosquitos get bigger and bigger," he murmured sleepily.

Amy swatted his head, ruffling his hair even more than it had been. "Not a mosquito, stupid. Moving gnomes."

That got Rory sitting up. "What?"

Amy gestured at the window with her head furiously. "Moving. Gnomes. I thought you got rid of them!"

"I did. And gnomes don't move."

Amy turned to stare at him. "Please tell me I'm not hallucinating."

Rory quickly climbed out of bed and moved to the window, staring out into the garden. "There's nothing there."

Amy was at the window in a flash. "What?"

"The garden's empty."

Rory was right; there was no sign of anyone having ever been there. Amy felt a pebble of doubt sink to the bottom of her stomach as she squinted at the rest of the garden, hoping to find some sign of what she had seen. Nothing.

"Grab a torch."

Rory looked at her in surprise. "What for?"

"We can't go looking for them in the dark."

"Them?" Rory repeated. "Amy, there is no 'them'. There's nobody there."

"I saw something."

Rory yawned. "You were probably dreaming."

"I wasn't," Amy countered, shaking her head. "No, I was definitely awake."

Rory didn't look convinced. "Are you sure?"

Amy glared at him.

Rory nodded calmly. "Ok, yep. You're sure. I suppose this means we're going early morning gnome hunting?"

Amy simply put her dressing gown on, not bothering to reply verbally. She heard Rory sigh and mutter something about lost sleep and an early shift before finding his own dressing gown and following her downstairs, picking up the torches as they went.

The back door creaked, as it always did, when it was opened. Tonight, though, Amy felt a shiver go through her spine at the low creak, unable to shake the feeling that she had walked into a horror movie. She shook her head to clear it of thoughts and stepped out onto the patio, feeling the cold along her toes in shock. She looked down and saw that she had forgotten her slippers.

Rory stepped out behind her and closed the door with another ominous creak. He clicked on his torch and pointed it at her face to see if she was alright. Amy simply nodded and turned hers on. Together they swept their torches over the garden.

The dark did strange things to the shapes that they were used to seeing every day. The finely clipped bushes became wild, unruly plants in front of a derelict house. The grass became fine blades pushing up from the earth and pointing at the sky, like a carpet of nails. The patio had more shadows and bobbles than usual, making it look like sandpaper under a microscope. They jumped at each unrecognisable shadow; a sleepy hedgehog almost gave them both heart attacks. It soon became clear that, despite the ethereal quality of a garden at night, there was nothing unusual to be seen.

Amy looked up at the stars and moon, wondering. She had definitely seen something.

Rory had followed her gaze. "Could you have seen aliens?"

"Aliens?" Amy repeated. "That look like moving gnomes and hang out in our garden at five o'clock in the morning?"

Rory shrugged. "Aliens are odd. We know that much already."

Amy was about to agree with him when an idea made her lower her head. "We haven't checked the TARDIS."

Rory flashed his light over the TARDIS quickly from top to bottom. "Looks the same as normal."

"No it doesn't," Amy countered, moving slightly closer, torch held in front of her like a sword. "The door is slightly open."

"You can see that, but you can't read the newspaper?"

Amy shushed him. "I'm serious."

Rory obediently fell quiet and followed her. When they were closer to the wooden door of the ship, he too saw what Amy had seen; the door was open a crack, and a dull light was infiltrating the darkness around them.

They shared a wary, nervous look.

"Shall we open it?" Rory asked.

Amy nodded and then, before either of them could rethink their strategy, opened the door. The couple were blinded by the light which, dull as it was, seemed unnaturally bright after the early-morning darkness, and they were forced to put their hands in front of their eyes.

From inside the TARDIS drifted voices, speaking quietly, almost as if they didn't want to wake anyone. Or disturb the peace.

Amy's heart leapt into her throat.

"Is that…?" Rory asked, voice husky, trailing off at the end.

Amy stepped into the console room, blinking furiously, and looked around. A man in a ragged tweed suit stood by the console, one hand resting over the controls, the other hanging limply by his side. A woman that was unmistakeably River Song stood facing him, though her view of the TARDIS doors was blocked by the Doctor. She also had her hand on the console, but underneath the Doctor's. Another man, one that Amy didn't recognise immediately, stood off to one side, his hands behind his back. He had a shock of blond hair and was wearing an old and dirty black hoodie with black trousers. He was looking between the Doctor and River with feigned indifference.

Amy simply stood there in shock, drinking in the sight of them both, wondering if they were a hallucination, while simultaneously internally jumping for joy. Had they returned?

Rory came to a halt beside her, seeking out her hand and clutching it desperately. "Am I going mad?" he murmured, quietly, so that the other three in the room couldn't hear.

"If you are, then so am I."

Now that she was getting used to the shock of the situation, Amy began to pick out words from their conversation.

"-not leaving him," the Doctor was saying, fiercely.

This, however, did not seem to deter River. "You can't keep him here, not with everything that is about to happen."

"Why?" The Doctor demanded. "What's about to happen?"

"Spoilers."

"Not much of an argument, is it," the third man chipped in, looking amused.

"You," River said coldly, barely glancing at the man, "stay out of this." She turned back to the Doctor. "You can't. He could escape, he could kill you, he could steal your regenerations, brainwash you-"

"I'll take precautions."

"Like you took the precaution of putting the shields up when you were being shot at?" River demanded.

"And for the record," the other man interjected, "I would never do any of the crude things you mentioned. My plans, if I were to make any, would be much more elaborate and refined."

River just glared at him.

"I'm taking him to Stormcage," River decided.

"No!"

There was a brief fight for control over the TARDIS. Amy instinctively ran forwards and pulled River back, while Rory lunged forwards and grabbed the Doctor, pulling both away from the controls. The two stopped fighting and stood still, shocked.

"Amy?" The Doctor asked hesitantly, almost as though he didn't believe she was real.

"Doctor," she greeted, grinning. "River."

"Mother," River replied, thawing out somewhat.

"Hello," Rory said awkwardly, hands still pinning the Doctor's arms to his sides. "You're back then?"

"Are you two all done fighting now?" Amy asked. "There's a lot of hugging to do."

No sooner had she said these words did Amy find herself ensconced in a group hug so enthusiastic that she thought it might never end. Or that she might be suffocated. They stood like that, the minutes ticking by, simply revelling in the fact that they were all together again, relief washing over each of them. And for once Rory did not remind the Doctor that there was a husband in the room.

After what seemed like an eternity and yet several seconds all rolled into one, a derisive voice cut through the atmosphere. "How touching. Are these your new companions, Doctor? You go through them faster each time."

The Doctor pulled out of the hug, annoyed, and just like that the spell was broken. Amy looked at the stranger, towards whom she had taken an instant dislike.

"Who's he?"

"He, Pond, is the other Last Time Lord."

Rory stared at the Doctor. "There are two of you?"

The Doctor indicated River. "Technically two and a half."

"I'm the Doctor's new pet," the stranger interjected.

"Pet?" Amy repeated, highly confused.

"His name's the Master," the Doctor explained. "You might remember him. Then again you might not. The time lines are bit wobbly there."

Rory stared at the Master, a look of dawning comprehension on his face. "Wait a minute," he said slowly. "I think I do actually know him. Harold Saxon."

"Who?" Amy asked.

"He had the American President assassinated during what was supposed to be First Contact," Rory explained.

"It wasn't supposed to be first contact," the Master said impatiently. "It was. And it was majestic."

"Then how come I don't remember it?" Amy asked him.

"The Doctor undid it all," the Master replied. "Using prayer. One of my most embarrassing defeats yet. I mean, come on, prayer."

"It never happened for you two, Ponds," the Doctor explained.

"Right…" Amy replied dubiously. "But he still killed the President. So why isn't he in prison or something?"

"And why was he even on Earth?"

"He," the Master replied pointedly, "was here for reasons beyond your comprehension, and he isn't in prison because he was dead."

"But he came back," River said pointedly. "He had followers to resurrect him. And every time someone attempts to imprison him or kill him he escapes or comes back. He's dangerous."

"So that's why you want to take him to Stormcage," Amy said, the penny dropping.

River nodded. "He needs to be contained. And the TARDIS isn't the place to do it."

"We agreed," the Doctor said tightly, "that it was."

"No, Sweetie, you said that it was and I went along with it until we got here."

"You helped me save him," the Doctor pointed out. "You must have thought he had some potential."

"I thought that I didn't want to be responsible for bringing a great species to the brink of extinction," River countered. "Not because I believed in him."

The Doctor's jaw tightened. "Well he's alive now, which makes him my responsibility."

"And I don't get a say?"

"You're not Time Lord."

"That doesn't mean I can't understand," River shot back.

"Actually," the Doctor said, anger beginning to show in his tone, "it does. You've already shown that by wanting to take him to Stormcage."

"He'd still be alive there."

If he had been human, the Doctor might have snorted. "Alive, alone, and free within five minutes."

"You do break out a lot," Rory pointed out to River, but evidently instantly regretted it in view of the glare sent his way.

Amy and Rory moved to the side, letting the couple argue it out between them. It was clear that something had happened when River and the Doctor had been in that parallel universe – wherever that had been – and that the human couple would have no chance of understanding it. The Doctor seemed in favour of keeping the Master on the TARDIS for however long it took to reform him, while River wanted to lock him up in the most secure wing of Stormcage (and hope that he never escaped and, if he did, that there would be a galaxy-wide alert), since there was no chance that he would reform and the Doctor would be unable to keep him locked up forever, given the events to come. Not knowing the Spoilers that River kept mentioning, or the man that the Doctor was defending, Amy and Rory began to feel slightly lost and rather useless in the argument. So they elected to watch instead, and hope that the others knew what they were doing. The Master, perhaps knowing what the outcome would be or not caring either way, simply watched, smirking and insulting them occasionally.

Finally, River threw up her hands in annoyed exasperation, swearing and muttering something about stubbornness and stupidity, before dragging the Master off somewhere further in the depths of the TARDIS. The Doctor turned around sheepishly to face them, fully aware that this had not been the homecoming that anyone had envisaged.

"He won't escape, then?" Amy asked, gesturing in the direction that River and the Master had left in. "He sounds dangerous."

The Doctor flapped his hands. "No, there's a brig."

"The TARDIS has a brig?" Rory asked.

"Of course it has a brig!" The Doctor replied indignantly. "What sort of a ship would it be if it didn't? A ship without a brig," he muttered, going to the other side of the console and pressing buttons, "ridiculous."

"What are you doing?" Amy asked, peering over his shoulder.

"Changing the security settings so that the Master can't get to anything important, or escape, or otherwise do… well, what he does."

"And that'll stop him, will it?" she asked.

"Should do," the Doctor chirped, not sounding too certain.

"It's just that even you don't know what's in every room," Rory pointed out.

"No," the Doctor agreed. "But – and here's the clever bit! – the TARDIS herself does, so she can help me keep him under control."

"Right," Rory said dubiously.

"Anyway," the Doctor said, "long story short, don't worry about him, he's harmless. Well, not harmless – who'd ever call the Master harmless? – but he's out of harm's way and should stay that way for a very long time, unless I decide otherwise."

"You're just going to keep him locked up down there?" Amy asked incredulously. "You'll never see him, never talk to him? After how long you waited for another Time Lord to come along?"

The Doctor pinched the bridge of his nose, suddenly looking very tired. "It's a very long story, Pond – it literally started centuries ago, and there are aborted time lines and paradoxes all over the place. Just trust me on this one, ok? You too, Rory. I know what I'm doing."

Rory and Amy exchanged dubious glances behind the Doctor's back as he went back to fiddling with the controls, regulating the settings to make sure that saving the Master wasn't some huge mistake. The two humans sat back and waited, bursting with questions, and neither sure which one to ask first. Meanwhile, the Doctor prepared himself, reinforced the mental barriers around the memories, which would no doubt be weakened during the constant barrage of questions, and formulated an edited explanation of what had happened to him. There was no need for them to know all the grisly details of his captivity and recovery, after all. He could only hope that they would be distracted by the constant allusions to Harry Potter that he was bound to make.

He smiled softly, letting their chatter wash over him, feeling himself relax. And, while he revelled in the fact that, for the first time in what felt like far too long, he was safe, he reached over with one hand, and flicked the button that put the TARDIS's shields up.