Here is my version of how Moffat could tie up the major threads that are still left dangling from the Moffat/Matt era.
I think it's important for at least the major stories to be satisfactorily concluded before Matt leaves.
I know most people probably don't even remember them by now, but these stories will be watched for years to come as box sets and downloads, and seeing all those unconcluded stories so close together could get confusing.
I think future sales, and the enduring reputation of this era, will be improved if he does manage to wrap things up in a satisfying way. Otherwise, the chance to make sense of this rather confusing era could be gone forever. (And remain irritating on rewatch when we then know they'll never be answered.)
Here's my version of how they could wrap up the arcs and still make it an interesting Christmas story, and not just a "question and answer" session.
(I didn't write this as a story, because I don't know what he has planned for the 50th. So this is mostly a "treatment" of what such an episode could be about. Although it does end with actual scenes.)
This would all be woven into one story, possibly starting with the Doctor and Clara investigating the Silence tunnels under the Earth. Prompted by what the Doctor saw in his time stream in Name of the Doctor. Let me know what you think.
Matt's Final Episode
Most of the main dangling threads involve the Silence anyway, so have him come up against the Silence again, one last time. Heck, in his final episode, a Christmas one at that, they could even call it "Silent Night."
Have the Doctor confront the Silence, and in the process have it revealed that the Silence aren't native to Earth, but actually invaded this universe through the cracks in time, cracks that they themselves created once they were here (that's a timey-wimey explanation that would appeal to Moff.)
They knew that blowing up the Doctor's Tardis would make him an enemy, and also knew that he was the only one (time traveler, protective of Earth) who would be a threat to them. They had come through the cracks on that first day, on Amy's wedding day when the Tardis exploded. Then used their time machines to go back in time so that they had "always" been here since the "fire and the wheel."
They created the tunnel system under the surface of the Earth and linked up a network of them to their fleet of time machines, that's how Earth was able to survive the "end of the universe" when the Tardis blew up. Their time machines were stabilizing it.
Then, when the universe was restored, they came with it. (Remember, the Starless universe would have happened when they first arrived with the original big bang that caused the cracks, then the universe would have been reset by the Doctor using the Pandorica. - That would even be a reason the Silence used their influence to get the "Alliance" to build the Pandorica to trap the Doctor, and coincidentally, give it just the right technology needed to reset the universe. Because, to the Silence, it had already happened.)
But, once they were established, it soon became apparent that they'd made an enemy in the Doctor. Especially after he enters his own posthumous time stream, and for the first time can see the Silence's "behind the scenes" plan all at once, woven all through his timestream.
That's why the Silence didn't want him to visit Trenselore. That's why "no living creature can speak falsely or fail to answer." With their whole plan and history laid out bare before his eyes as he rescues Clara, the Doctor now knows how to defeat the Silence, and send them back to their own universe.
That's what they were trying to prevent. That was the reason for their "endless bitter war" against the Doctor. A war he hadn't even been aware of. (By seeing all this in his own time stream, he could remember it, because he wasn't just seeing the Silence, but rather their influence. So he doesn't forget.)
Now, at Christmas, all this comes out as the Doctor finally confronts the Silence with all the information in hand. He now understands why they created River. For one, they knew they already had created her, since she was the one who blew up the Tardis to let them in. (Another timey-wimey effect for Moffat.)
But they also used her as a distraction. Mystery piled on mystery, feints and dodges meant to confuse him and keep him occupied. A woman to keep him intrigued and distracted. A puzzle with the pieces deliberately rearranged and unconnected, so that he never could solve it, but would keep wracking his brains to try.
The girl in a spacesuit, a spacesuit in a lake, (yes, he'd got in a good shot in the war with that "kill us all on sight" command, but it hadn't taken long for them to retreat and regroup,) and basically creating a competitor who could give him a run for his money. - At a time when there were no more Time Lords, no Master or Rani to challenge him, they made him a Time Lord, someone who, like him, had no limits, who could travel in time, jump out of windows, and make him exercise his brain, because she could keep up with him, and even be one jump ahead.
"So all this time, River was just a distraction?" the Doctor demands, outraged.
"No, she was needed to pull the lever, to explode the Tardis and let us through."
"Under post-hypnotic command from you."
"Yes."
Then the Doctor looks past the Silent, and starts to give a little smile. "Then I think it's only fair that she be the one to send you back."
The Silent whirls, and behind him, unexpected, stands River, and outside, a second Tardis appears in space, the date of Amy's wedding flashes across the bottom of the screen. The second Tardis explodes, ripping a huge crack across the heavens, a fleet of Silence time ships come pouring through, flowing down to infest a defenseless Earth.
And as the last of them disappears into Earth's atmosphere, the crack closes. Then first Tardis explodes, ripping a new crack across the sky.
And inside the rocking, now time-protected console room of the second, exploding, Tardis. River holds onto the lever and grins a satisfied grin at the fading Silent. "Sauce for the goose... Sweetie."
Outside, the Silence are sucked off Earth and go tumbling back into this new Crack in time. As the last Silent ship disappears the crack closes, and the Tardis is left hanging alone and peaceful in space.
The Doctor grins and bounces on his toes. "Controlled explosion," he explains to Clara.
"So," Clara says, unsure, "none of it ever happened now?"
"Oh no, it all happened, it's just a closed time loop. Well, not a loop loop," he whirled a circle with his finger (like he did in Time of Angels) but more of a loop loop." He explained with a smile, swooping his fingers.
Clara looked at River, "Did that make any sense to you?"
"Yes, actually." River smiled. "This segment of the timestream simply began and ended at the same point," she made a line with her finger, looped it in the middle then continued the line.
"Simple really," she said, grinning at the Doctor.
The Doctor clapped his hands and twirled, "All taken care of then! Where to next?" he reached for the controls, happy.
And the console started sparking with running electricity. Suddenly a lightningbolt came out of nowhere and struck the Doctor full in the chest. He staggered back, looking down at his burnt chest. "I didn't see that coming," he fell back.
River whirled, and shot the one last Silent who they had all forgotten was there.
And this is when the Doctor regenerates.
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(What do you think? Would that answer enough questions? For more see the first comment below.)
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