//------------------------------//
// Jelly Baby? 
// Story: Allons-y! 
// by Sixes_And_Sevens 
//------------------------------//

“...Doc?” Applejack asked, leaning over his prone form. He lay there, staring at the ceiling.
She prodded his side with a hoof. “Are ya okay?”
He shook his head in an attempt to clear it. “Ow.” he grimaced. Looking up at Applejack, he said,“What… what just happened?”
She frowned. “Ah reckon you oughta be tellin’ me that.”
“I’ve no idea. Look, Twilight told me you’re the Element of Honesty—”
“Technically, we had t' put them Elements back where they came from. These days I’m the Councillor of Honesty, or, uh, the Magistrate, or summat like that.”
“Whatever. Tell me if I’m lying when I say that I don’t know why Ditzy reacted that way.”
“Yep.”
“... What?”
“Yes, yer lyin’.”
“I am not!”
“Yep, there’s another one.”
“I never lie!”
Applejack actually flinched. “Whoo-we! Now that there’s a WHOPPER of a whopper!”
The Doctor sighed, frustrated. "Look, will you go up to the kitchens and get me an icepack?" he asked. "I can already feel my cheek swelling up."
"Fine," Applejack said. "But when Ah get back, y'all'd better be ready to explain yerself real good." She trotted quickly across the room and went downstairs to find the kitchen.
The Doctor sat back, gloom overtaking him. There was so much pain he had wrought, so much suffering he had caused. He didn't realize there was so much that he was starting to forget it all. He glared at the hologram. It smiled back, mocking him with the image of him amnesiac former self.
Amnesiac.
Wait a second.
“I don’t remember.”
Applejack looked at him in confusion as she trotted back up the stairs. “What don’t ya remember?”
“Well, if I knew that, I wouldn’t have forgotten it, would I?”
“She rolled her eyes at that, hoofing him the icepack. “Alright, then. Ya forgot somethin’. How do you remember it again?”
He winced as he put the ice against his sore cheek, then twisted up his face in thought. “Well, generally speaking, anything from that incarnation--" he gestured vaguely at the hologram, "--is a no-go zone. My personal timeline underwent quite a lot of... let's call it interference. I developed amnesia several times, almost as a defense against the conflicting memories. No, I think this is something I just need to work out logically…” he glared pensively at the new time rotor, green electricity dancing through it.
Disjointed memories, thoughts, and emotions flittered through his mind. Ditzy’s uncharacteristic anger… her husband had been a Time Lord. Had he been the Master, perhaps? Or some other enemy? Someone who would've recognized that face, and told Ditzy about it... Not likely, but it was a lead. 
Whoever it was had gone to war. Very likely, Ditzy had been referring to the Time War. Given that Equestria was in a whole other universe, it must've looked like a good place to escape from it. Pity he hadn’t thought of that himself. Had he? 
Hm. What else was there? Feelings! Very important, always trust your gut, Doctor. Her house made him feel very odd, almost domestic. Eugh.
Older memories began to surface. A young lavender unicorn, her mum’s eyes and her dad’s coat… a wedding… a chance meeting… a courtship… a proposal… wait. A wedding?
The Doctor’s eyes flew open. “Oh, spack.”
Applejack leaned in. “What? What’d you do ta Ditzy?”
"Oh, this, this is bad," the Doctor said, leaning against a railing, letting the icepack fall to the floor. "This is worse than bad. Think of the three worst things you can think of, glue them together, that's not even close to how bad this is!"
Applejack sat down and folded her hooves. "Ya think y'all can be a li'l more specific, there?"
The Doctor turned to her, pain and fear in his eyes. “I… may have married her.”
There was a long pause. “Y'all did what now?” Applejack squawked, torn between anger and disbelief.
“There was a war," he babbled. "Biggest war in the cosmos, in the multiverse. I ran away, tried to escape, hid out here for awhile. I hid the TARDIS, got a job, tried to blend in, but I never thought that anything like this would happen!”
“How exactly do you forget that you have a wife?” Applejack demanded, “AND a daughter,” she added, after a moment’s consideration.
The Doctor waved his hooves frantically. “Like I said, my personal timeline got mucked up. My past became unstable, fixed points became unfixed, people suddenly stopped having ever existed! For literally an entire century, I was wandering around the Earth with no memories of who I was!” He was trembling now. “So now, there’s just a huge chunk of my personal history that I can’t remember, because it just doesn't exist!”
Applejack's jaw was hanging open as the Doctor continued to panic. She closed it with a snap. One of them had to be calm in this situation, and it didn't look like the Doctor was about to get a level head on his own. “Well," she said. "Yer back now. That’s a good start.”
The Doctor stopped and looked down at his hooves. “But now she hates me,” he said quietly.
The orange mare scoffed. “Ditzy? Hate? Ah don't reckon that mare's ever done that afore. Sweet as summer. That said—” her face hardened again. “You answer me this, and if you answer wrong, you can jes’ fly this spaceship away.”
She glared sharply into his eyes. “Do you love her?”
He paused. The memories were flowing back, now that the plug had been pulled. He let them flood his mind. He remembered seeing her for the first time, back when he was posing as a professor and accidentally put all his things in the wrong office. He remembered her walk, her smile, her laugh— oh, that laugh, all the times they had laughed together— he remembered the time he'd stood up for her at the university, and as a thank-you gift she filled his apartment with banana-nut muffins. He had told her they were his favorite five months before.
He remembered her mind, oh so clever at crosswords and understanding the universe— and muffins, he supposed—  remembered that sharp glint in her eye when she had got an idea.
He remembered all the times they had spent together, good and bad.
He remembered quitting his post at that prestigious university because she had been cut from the staff.
He remembered moving to Ponyville, sharing rooms with her college roommate until they had been able to buy a house.
He remembered their daughter.
He opened his eyes and let loose his tears over his smiling face. “Yeah. Yeah, I really think I do.”
Applejack studied him for another long moment. Then, she suddenly smiled and stepped away from the door. “Go get ‘er.”
“You are absolutely brilliant, you know that?” he said, beating a rapid path to the door. At the threshold, he paused and, glancing back, added “Just make sure that no one touches the console while I’m gone. Or… anything else in here, actually.” he dashed out.
Moments later, he popped his head back in, grinning coltishly. “Oh, and Applejack? Thanks."
“Quit stallin',” Applejack cried in mock anger, waving her hat at him. He winked and ran out again.
Donning her hat and chuckling, she settled down to her guard duty.