My own personal theory about the events of the 50th anniversary, and the only way I've found to be in any way satisfied. Warning, massive spoilers; also, not a standard fix-it. You have been warned.
"Doctor? Doctor!"
The Doctor woke with a start to see Clara leaning over him, her face scrunched up in concern and maybe a touch of irritation. It cleared quickly when she realized his eyes were open, and she punched him in the shoulder.
"Ow!" he yelped. "Was that really necessary?"
"Yes," she snapped, leaning back. "You scared me half to death, lying there like that."
"Better half dead than completely," he said easily, springing to his feet before holding his hands out to her. "Where are we?"
"How should I know?" she asked, glancing around at the dense fog surrounding them. "All I remember—"
"Oh, minor retrograde amnesia, I'm sure it'll come back to us in a moment," he said, pulling out his sonic screwdriver and scanning the surroundings. The readings came up completely blank, and he hit it against his palm a few times.
"You're awfully chipper," she said, eying him. "Especially for someone—"
"Of course I'm chipper, Clara," he said. "It's out there! It's out there somewhere, somewhere I can find it. Somewhere we can find it!"
"Find what?" she asked, peering around.
"Gallifrey!" he exclaimed. "Oh, don't tell me the memory patch affected you too. Shouldn't have. Should only have been my other selves."
"Other selves?" she asked as he turned the sonic screwdriver on her. "What other selves? Hang on, wait, what do you mean Gallifrey? You said that it burned in the War."
"It did," he said. "But then it didn't. Oh, you were right, you brilliant girl. So right."
"Right about what?" she asked, sounding completely out of sorts.
"About me!" he said, spinning around with his arms outstretched. "The Doctor, the man who saves people. And I saved them, all of me, every regeneration, frozen in hope, locked in a painting."
"A painting," Clara said flatly, staring at him oddly.
"A painting," he affirmed. "All those children, they're alive, somewhere…I just have to find them."
"Wait, hang on, just…go back," Clara said, holding up a hand and closing her eyes. "You said Gallifrey had to be destroyed, that they would have smashed the universe apart if they weren't."
"Oh, that was just the council," he said, attempting to scan the area again and frowning when the screwdriver still gave no readings. "If they're removed from the War and the Dalek threat, then they can be reasoned with, or deposed…either way, it can be fixed."
"That's not what you said," Clara said slowly. "You said it was everyone. You said even the children were just corruption still baking, conditioned from birth that they were better, superior to any other race or species, even before the Academy."
"No…no, that's not…that's not what I…"
He trailed off, a memory suddenly coming back to him.
"It would be so simple if it was just the Council," the Doctor said with an irritated sigh. "Like a diseased organ that could be removed, replaced with a healthy transplant that could save the body. But it wasn't. That disease, that arrogance, it had spread through the whole society. No one was safe. My family distanced themselves from me, disowned me, all except Susan, because the disease was so widespread that the body was attacking itself. I was abused, and manipulated, and shunned…because I saw the disease for what it was: the eventual death of the oldest society in the universe, done in by its own inflated self-worth. I wish it was the Daleks who were at fault. I wish that it was just a corrupt administration driven to desperate measures. But it wasn't. The Final Sanction had been devised long before, acknowledged and supported by the masses, or at least the masses they felt mattered. All they were waiting for was an excuse. If it wasn't then, it would have been later. And I still would have had to stop them. I would always have had to stop them."
"But…but we saved them…" he said weakly. "We got out of the time stream, and we went to a museum…Zygons were hopping out of paintings…and then I met my other selves and we saved them."
"By freezing them in a painting," Clara said.
"Yes, we froze them in a painting, Clara," he snapped, his inexplicable uncertainty making him tetchy. "Try and keep up."
"How did we get out of the time stream?" she asked quietly.
"What?"
"How. Did we. Get out. Of the time stream?" she repeated slowly.
"We…well…we…"
"You don't remember, do you?" she asked gently, as horror began to rise up in him. "Didn't you ever wonder about that?"
He looked around now, really looked, and saw what he'd been avoiding since he woke up. People appeared and disappeared around them, dancing through the fog, like ghosts on a moor. They were all familiar…of course they were, they were him. Moments of his life were being lived around him, silenced by time and relative dimension.
"We never left the time stream," he whispered hoarsely. "None of it happened."
He sank to his knees, the heavy weight of his burden of guilt becoming impossible to bear after the taste of freedom. It could never have been real…Gallifrey could never be saved. He knew that, and he knew he'd done the right thing. Now that he actually examined the experience, none of it made sense…the way they'd somehow included all his incarnations, even his future one…the way they'd been able to reach Gallifrey at all through a time lock without being driven insane like Caan…the way he couldn't remember how they'd gotten out of the time stream—or, for that matter, what they'd actually done about the Zygons. None of it happened, none of it was possible; from the moment he'd leapt into the time stream, it had all been a lie. But in a universe of his own creation, in the crystalline beauty of wishful thinking, it was achievable…and it made the harsh reality that much more painful.
His belief that there was no god outside the universe, no higher intelligence dictated order in chaos, was cemented in that moment. Because what God would devise this?
In all honesty, in my dream world, Moffat would be replaced by a writer with some actual sense, and this is exactly how the next episode would start, followed by the Doctor somehow having to sacrifice a regeneration to get himself and Clara out of the time stream, thereby giving us Twelve and a return to sanity. But that's just me.