Chapter Forty One: The Beginning of the End.

***

Plymouth Forward Base POW facility. May 5th. 2030.

On the edge of the city of Plymouth, in a dark room far from any windows, a green unicorn mare in purple robes with the stylised image of a purple star in a sun was tied to a chair. In front of her was Errant Flight and Major Redmond, the former looking calm and collected and the latter looking furious.

The mare was named Gentle Flower, and the lack of cutie mark visible underneath her robe was evidence enough that she was a Converted. Had you asked her, she would have been proud that she, a mere Converted who had only been a unicorn for six of her twenty three years had managed, through diligence and study, to become part of Twilight Sparkle’s famous Archmagi. She had been one of the handful of Equestrian survivors on the Illustrious, having been captured by human forces sweeping the ship after she docked.

Being an Archmagi, she was automatically one of the most important ponies they had captured. It was quickly decided to let Redmond and Errant Flight interrogate her personally - Redmond was one of the highest ranking personnel on site, and Errant was one of the highest ranking personnel to have been aboard Illustrious during the mission to reclaim her.

“I’ll ask again,” Redmond said, his voice inches away from being a bellow. “What the hell were those bodies being used for?!”

“I keep telling you, Mr Redmond sir, that I’m not at liberty to tell you why we needed those bodies,” Flower replied, a slightly bemused smile on her face. "I really do wish I could tell you, believe me. It would make me very happy to be able to do as you ask, because I can tell this is all very upsetting for you..."

Redmond lashed out, the back of his hand striking Gentle Flower across her face. She blinked, then smiled again.

"... but I'm afraid these are orders direct from Commander Twilight Sparkle herself." The Converted grinned slightly. "So you see, very important."

"Yeah," Redmond muttered. "I see."

He turned away, leaving Errant Flight to talk to the Converted. The plan was the old "good Guard, bad Guard," plan (though Redmond called it "good cop, bad cop") with Errant as the good cop. Somehow Redmond thought Errant could get through to this Convie idiot.

"Listen," Flight said quietly, trying the sympathy approach. "My friend isn't very happy. He's lost a lot of his friends today and the Illustrious thing hasn't helped."

"Oh, I'm sorry to hear that," Gentle Flower said honestly.

"Yeah," Errant continued, slightly sourly. "Anyway, you've got to see it from his point of view. Ponies did this to humans. Those bodies..." He shuddered slightly. "Did you see them?"

"Oh yes," Flower said quietly, her smile fading. "A dreadful business. Quite horrid."

"Yes, quite," Errant said, trying his best not to get angry. He was playing good cop, he reminded himself. "So you see why knowing why it happened might help his unhappiness. Make him realise there was a reason. I mean, there was a reason, wasn't there?"

"Well," Gentle Flower said, looking somewhat ashamed of herself. "Yes and no." Errant raised an eyebrow as she continued. "The bodies we needed. The state they were in isn't entirely because of that though - though a lot of it was. Some of the Guards aren't as... nice... as we are."

"So they mutilated the bodies of revenge," Errant Flight said quietly.

"That wasn't why we had them, though," she said quickly. "It was... it was for an important reason. Some of the injuries were necessary too."

"What do you mean?" the Pegasus said with narrowed eyes.

Gentle Flower gulped. "I - I can't tell you. I am sorry. I wish I could relieve your friend's unhappiness and tell him all about it, but I have my orders, you see."

Before Errant could respond to that, Redmond stepped up to him and whispered something in his ear. The Pegasus frowned, then grinned.

"Alright," he said softly. He turned to Gentle Flower. "We're called away on other duties. We'll be back to continue this conversation."

"I'd greatly like that," Gentle Flower said with a smile.

Errant Flight and Redmond exited at once. Gentle Flower let out a sigh of relief.

"By Her mercy," she said quietly. "I thought they'd never leave."

There was an almost ringing silence in the room that seemed to mock Gentle Flower, and almost reflexively, she gulped. She wondered vaguely how long they would leave her here...

***

Plymouth Base Landing Pad.

The transport helicopter descended from the sky agonizingly slowly, at least in Rarity’s considered opinion. She didn’t know much about the aerodynamics of the machine - at least when compared to Pegasi flight or the airships of her native Equestria (and, she supposed with a grimace, the Zeppelins of this world as well) - but she figured that it had to be able to come down at a faster rate. It just had to.

“Is she here yet?” the voice of Pinkie Pie said quickly from behind her. “Is she here yet? Is she here yet? Is she here yet?”

“Not yet!” Lyra laughed, trying to keep the party pony from bouncing high enough to meet the copter on it’s way down. “In a minute!”

Rarity, while she was attempting to be more dignified than Pinkie, couldn’t help but agree with the sentiment her friend was expressing. It had been too long since she had seen Twilight, since any of them had seen Twilight. She was as impatient to see their friend as anypony. Still: a little dignity couldn't hurt...

The entirety of Everfree team was here - those of them who were left, anyway. There was a notable absence in Sapphire Steel, and the dour visage of Desert Wind was testament to the open wound at the heart of the squad. Behind Wind stood True Grit, who had taken over as his steadier. In addition to them, Rainbow, Ditzy and Fluttershy were all present.

The copter continued its descent, the rotors slowing as it finally touched down. A moment later, the side door opened, and a half dozen human and pony soldiers in black gas masks and black haz-mat suits exited, jogging past Everfree squad quickly. A moment later, Twilight herself stepped off of the copter. She looked tired and slightly thinner than the group remembered, but otherwise unchanged.

"Hey everypony," she said quietly when she saw her friends.

Pinkie's reaction was immediate - the pink party pony charged right at Twilight, hugging her so tightly that her head began turning blue. Pinkie immediately began blabbering.

"Twilight you're back thank goodness we missed you there's been so much going on it's been so horrible I wish you'd been here there was a battle on a big boat and..."

"Let her breathe, Pinkie," Applejack said with a tired grin. Pinkie immediately released Twilight. She gave one final grin and bounced back, letting the others come forward.

Applejack stepped up to Twilight and hugged her briefly. "Good to see you sugarcube."

"Are you ok?" Twilight asked her friend.

"Couple o' problems," Applejack said with a shrug. "Tell you later, maybe."

Next up was Lyra. She hugged Twilight silently, before stepping back, a bittersweet smile on her face.

"Good to see you, Lyra," Twilight said.

"And you, Twilight," Lyra replied.

Rarity hugged Twilight almost as tightly as Pinkie had, but she said nothing, merely smiling at her, a small tear forming in the corner of her eye.

"That helicopter was really slow," Rainbow commented as she hugged her friend. "Couldn't it have gotten you here any faster?"

"Not really," Twilight replied, chuckling slightly. "Maybe you could have."

Rainbow laughed at that. Fluttershy and Ditzy both hugged Twilight silently as well, their expressions - both full of joy - saying more than enough.

True Grit saluted Twilight, the former Guard still clearly uncomfortable with the levels of familiarity the others had shown. Laughing, Twilight hugged him, and he hesitantly hugged back.

"Looking good, Grit," she said with a short laugh. "Maybe try to chill out a bit."

"We aren't here to chill out," the harsh voice of Desert Wind cut her off. "We're here because you said you had a way into Equestria to end this bucking war."

"Hello Desert Wind," Twilight said, frowning slightly at the stallion's greeting. Her eyes swept the group, her frown deepening as she noticed an absence. “Where’s Sapphire Steel? Is she…?”

The words died on her lips as she saw everypony’s expression’s, her own face falling and tears springing to her eyes.

“Oh no,” she said quietly. “Oh no…”

“Yeah,” Desert Wind said harshly. “So you’ll forgive me, Sparkle, if I don’t want to spend time reminiscing when we could be working on a way to bring this bucking war to an end, preferably an end involving me ramming the other Sparkle’s head into a wall repeatedly.”

Twilight nodded once, her eyes still watering.

“Where’s Elliot?” she asked. “It’s him who’ll have to see this.”

“Not just me,” came the familiar voice of the Avatar of Albion, as Elliot walked up to the group, a group of ponies and humans - including three very familiar figures - behind him. One of them was a white unicorn with a blonde mane, dressed in a stylised version of Night Guard armour. The other two were humans, one a slightly heavy-set Japanese man in a grey suit, the other a grizzled-looking military man in urban camouflage gear. The other two men were having a conversation with Major Redmond and Errant Flight, who was stood a small distance away from the landing pad, near the entrance to the POW facilities.

“Twilight,” Elliot said with a grin, “I believe you’ve already spoken to the Council.”

"Yes, of course," Twilight said, nodding respectfully at the group. "It's an honour, sirs."

"Sparkle," Prince Blueblood said politely. "What rank did you say she was, Commander?"

"Strictly speaking, Everfree squad are part of my spec-ops units," Elliot replied without looking at the Unicorn. "No official rank. Sparkle here was assigned as the leader..."

"Then Lieutenant will do," Blueblood said. "She'll need some rank for the paperwork and an officer rank seems fitting. Dinky, make a note."

"Will do, sir," a purple Unicorn mare said from behind him, jotting something down. Twilight blinked in surprise as she recognised a grown-up version of Dinky Doo, Ditzy's daughter. Ditzy herself stared at her for a moment, before turning away from her with an embarrassed expression when the Unicorn threw a dirty glance her way.

"Then there's the other members of Everfree squad," Blueblood continued, having apparently not noticed. "I believe 'operative' will cover most of them, except for Sergeants Rarity and Applejack who, I believe, have both been in command during Sparkle's research leave. And of course, Flight Officer Fluttershy and Flight Lieutenant Rainbow Dash of Grey Squadron are already listed."

A flicker of emotion passed over Dinky's face as she noted another mare among the group with a frown.

"Yes sir, they are, along with Flight Lieutenant Doo," she said, looking annoyed.

Ditzy Doo looked even more upset, but said nothing.

"Yes," Blueblood said with a frown, looking slightly guilty. "In any case. You've all done sterling work during the Plymouth campaign, but my understanding is there's something more important waiting for our attention?"

"Yes sir," Twilight said quietly. "There is."

"Excuse me," interrupted the voice of Major Redmond, walking up to the group, the two human councillors behind him. "Before your demonstration, Sparkle..."

"Lieutenant Sparkle," Elliot corrected him with a slightly smug expression.

"Lieutenant," Redmond repeated, frowning slightly. "We need your help with a delicate matter."

"What do you need?" Twilight asked, frowning. She had only been back for a few minutes and already there was something that needed her help - a battle?

"Your signature," Redmond replied with a smug grin of his own.

Twilight blinked in surprise. That hadn't... quite... been what she had expected...

***

Gentle Flower hummed to herself quietly. She didn’t really like being alone - it left her a bit more time to think than she strictly enjoyed, and she felt guilty that she couldn’t help the two who had been questioning her.

It wasn't that she didn't want to tell them - she did! Really she did! For one thing, much as she didn't want to believe it (she always thought ponies, at least, should be nicer than that) she was reasonably certain that they would probably at some point begin hurting her to retrieve the information. Also, it just wasn't nice keeping anything from anypony - or any human... no, the word was "anyone", wasn't it?

She frowned. She wondered precisely why thinking about humans and human language made such an odd tingle at the back of her skull. It was almost the same as the feeling she got when she thought about the hurting she was anticipating - a dull buzz that seemed to be trying to be more, and yet felt very far away. Still, the thinking about humans was different - almost like a stinging. It felt… bad, which was odd in itself because bad was a thing she had almost forgotten the feeling of.

Maybe it would be better to tell them... some small part of her thought. At once, the stinging got more pronounced, and she winced.

No, she thought suddenly. We were told to say nothing, and so we'll say nothing.

She was so distracted by the stinging, even as it receded, that she didn't notice the haggard looking pony entering the room until he already had. Once he had entered, she frowned at him. He was a Unicorn, haggard and tired looking, wearing a black outfit that she didn't recognise.

"Hello," she said at once. "What's your name?"

"Well Spring," the pony replied at once, a slight grimace crossing his face. "Guard Battalion two-twenty four, assigned to Plymouth campaign."

Gentle Flower's eyes widened in surprise - an Equestrian Royal Guard, here?. "Goodness! What are you doing here?!"

"Special directive, classified," Spring said with a slight frown. "Came to see how much you told them."

"Nothing, as per my directives!" Gentle Flower said at once. "I wish I could, but..."

"Good, you've followed your orders," Well Spring said, cutting her off. "Need you to tell me everything."

"What? Why?" Gentle Flower asked, frowning slightly. That didn't make sense...

"New orders," Spring said, holding up a piece of paper. “I need to know what you know so Command knows what’s at stake here.”

“Those…” Gentle Flower said, but then she breathed in sharply. The signature authorising the orders was none other than Commander Twilight Sparkle itself. “Oh my!”

“Yeah,” Spring said. “You see how high up this goes?”

“Yes, yes of course,” Gentle Flower said quietly. “What do you need to know?”

***

Outside, about five minutes later, a sick looking Wallace Springfield trotted over to Redmond and Errant Flight. The two had been joined by the Undead, the Dead Man who had recruited Springfield, and was the head of the Dead Men cult.

“Success?” the Undead asked quietly.

“Sir,” Springfield replied quietly.

“How bad was it?” Errant asked, frowning slightly at the sight of the sick looking pony. If it was bad enough to make a Dead Man look ill (they were notoriously hardy) then it must have been bad.

And then Springfield told them.

It was bad.

***

Plymouth Forward Base Mess Hall.

“... and then the buckers scattered like clouds!” Rainbow finished, grinning widely.

In the mess hall, Twilight sat with her friends. It had been a long flight and Elliot had convinced the council to allow her a short break with her friends before her demonstration. Rainbow Dash had just been explaining her rainboom and the circumstances of her injury to Twilight, who was understandably a bit worried.

“It was so scary,” Fluttershy said quietly. “I was so worried when Rainbow started falling.”

“Yeah, but you and Dark Wing had my plot,” Rainbow replied with a grin.

Twilight smiled weakly. It sounded like her friends had been through hell together - she only regretted that she had not been there.

“Course, with the deck cleared by Grey, Everfree was clear to land on the Lusty herself,” Applejack continued, taking up the story with a grin.

“The ’Lusty’?” Twilight said with a frown of distaste.

“Old nickname,” a new voice spoke. Hell Blazer and Doctor Clock Smith appeared, though the older pony was silent. Hell Blazer had a cigarette in his mouth and took a contented drag. “Hits the spot.”

“Those will kill you,” the Doctor said quietly. “You know that, I trust?”

“Handy thing about being a Converted,” Hell Blazer said with a slight expression of distaste. “New lungs. No history.”

“I believe True Grit - our True Grit,” the Doctor added with a glance at the newcomer Grit, who nodded sheepishly, “pointed out the dangers of smoking as much as you do with a pony body?”

“Cry me a river, Doc,” Hell Blazer said with a grin.

“Why would anyone name a ship ‘the Lusty’?” Twilight asked with a frown.

“You’ve never met sailors, have you Sparkle?” Hell Blazer asked with an amused grin. The grin soured slightly. “They’ll be ages fixing her up after this, though. And the smell…”

“Yeah,” Pinkie said unexpectedly. “That might take a while to get out.”

“You mean…?” Applejack asked, and then she too took on a morose expression as Pinkie nodded.

“What happened?” Twilight asked. The rest of Everfree team exchanged uneasy glances.

“Bodies,” Desert Wind said bluntly. "Human bodies. Mutilated. Experimented on."

There was a brief pause as Twilight registered this information. "I..." she said, stuttering somewhat. "I... just... why?"

"We don't know," Hell Blazer said quietly. "We're gonna find out."

There was a pause full of

“Excuse me,” Ditzy Doo said, speaking up. “Doctor Clock Smith, can I talk to you in private?”

The Doctor frowned, and glanced at Hell Blazer. The other pony shrugged with an expression of resignation, and the Doctor sighed.

“Of course Miss Doo,” he said quietly. He walked a little away from the table, and Ditzy walked over to join him.

“What’s that all about?” Rainbow asked, frowning after them.

“It’s a long story,” Hell Blazer said quietly. “And it’s theirs, not mine.”

***

When Ditzy reached him, the Doctor was quiet. He didn’t know quite what to expect, but he did know that he wasn’t prepared for this. In fact, he was fairly certain that he could never be prepared for this.

"Hello again," she said when she reached him, an odd note in her voice.

"Hello, Miss Doo," he said, trying not to let her proximity bother him. "What can I do for you?"

There was a moment's pause as she stared at him, a slightly sad smile forming on her face.

"I know," she said after a moment.

"Know what?" he asked at once, a cold shiver running down his spine.

"I know that you're the Doctor," she said patiently. She knew he was stalling her - it was, she supposed, his right.

"There are many Doctors in the Equestrian Resistance," he said, feigning ignorance. "You'll have to be..."

"You're my Doctor," Ditzy added, cutting him off. "Doctor Hooves. The Time Lord."

The Doctor's voice died away, and his frown deepened, showing off his wrinkles. Ditzy smiled sadly.

"How did you know?" he asked after a moment. He wasn't entirely surprised - Ditzy had always been smarter than most ponies thought she was - but still.

"You told me about regeneration," she said quietly. "Or my Doctor did. And I recognised the sonic screwdriver on the Illustrious when you used it."

His eyes glanced involuntarily down at the screwdriver, still resting in his battered leather bandolier, the last remnant of his Ditzy.

"I never used this model in front of you," he said quietly.

"No, but you did before, and it's still in the display cabinet in the TARDIS," she said quietly. "Along with a jacket a lot like that one, with a scarf a lot like that one too."

He said nothing for a long moment as they stood in silence. Ditzy apparently seemed patient enough to let him speak first.

"I didn't want to speak to you," he said to her after a moment. "I was... I was ashamed."

"Why?" Ditzy asked, looking confused.

"I regenerated after you died," he said. He shook his head. "After she... my Ditzy... died." He paused, looking angry at himself. "Thinking of you as her will not help me."

"Why did you change?" she asked, looking concerned - so much like his Ditzy that it almost hurt to look at her. "Were you hurt?"

"Not physically," the Doctor said quietly. "But regeneration can be triggered by choice. My choice was this form." He paused, trying to collect his thoughts. "It is the pony equivalent of a body I wore in humanoid form many years ago, during a greater, more terrible conflict."

"I didn't think you could do that," Ditzy said quietly.

"An exact replica, no," the Doctor replied, equally quietly. "But my previous pony form was a rough portmanteau of earlier bodies in terms of some physical and mental traits, so revisiting past forms and mindsets is obviously possible. With enough practice, I might even be able to replicate entire humanoid or pony bodies I have worn before."

"Why this one?" Ditzy asked.

"I..." the Doctor began, then he paused, clearly thinking how best to explain it. "You recall I may have briefly mentioned the war." Ditzy nodded. "During that time, I wore the humanoid version of this face. I regenerated then because if I did not, the universe would die - but I was really prompted by the death of a young human girl I had just met. Her death showed me that I could no longer hide." He paused, his voice cracking slightly with emotion. "When my Ditzy died..."

"It was the same sort of thing that made you become this person before," Ditzy finished for him. He nodded.

"And I swore I would do everything I could to stop Solamina," he said quietly. "Unfortunately, whereas in most cases I can usually figure something out, magic is not my area of expertise. I have managed to do my part, convince others to fight, lend help as I did on the Illustrious... even grant small tidbits of technologies to the human forces, though with their limited resources all I managed was more efficient solar energy panels, some new ways to produce ammunition and a few new kinds of energy and food-production technology - but I cannot end the war as I had hoped." He looked downcast. "As I failed Ditzy before, I now fail the entire human race, as well as all free ponies."

Ditzy smiled and put a hoof on his shoulder. He looked up and smiled softly.

"I know you're a good pony, Doctor," she said quietly. "And I know, whatever you've done, it was the best you could do. And knowing you, you won't stop until Solamina is stopped." She paused. "Just promise me something."

"If I can," he said quietly.

"When this war's over," she said quietly, "and if we're all still alive - promise me you'll find somepony to travel around with? If there's one thing I know, it's that you're not happy being alone."

The Doctor looked pensive for a moment, and then he sighed.

"If I survive, then yes," he said slowly. "I promise, I will find someone - or somepony - to take into the TARDIS with me."

Ditzy smiled, and hugged him.

"For what it's worth," she said quietly, "I know that your Ditzy would have been really proud of you."

Slowly, he reached up and hugged her back, closing his eyes. A single tear escaped from one eye, though he would never have acknowledged it.

"Thank you," he said quietly. "That means... that means more than you know."

The hug broke a moment later, the tear still lingering on the Doctor's face. He ignored it, eyes now focusing on four figures entering the mess hall. Ditzy frowned and turned to look in the same direction, her eyes widening slightly when she saw who it was. Elliot had entered with the council members, and they were talking with Twilight now.

"Ah," the Doctor said quietly. "It appears the time has come for Miss Sparkle to begin her demonstration."

***

A field near the base, five minutes later...

Twilight stood in front of the group. As well as the council and David Elliot, all of her friends were present, their expressions encouraging. As well as them, she could see Hell Blazer and the Doctor, both of whom wore neutral expressions.

"Alright," Twilight said, trying to get everyone's attention. "I need everyone to listen, because this is important." She took a deep breath. "I need every single one of you to concentrate on where you want this portal to come out. For ease of reference, I want everypony and everyone to concentrate on this world's Ponyville, ok?”

“Why?” Blueblood asked, narrowing his eyes.

“It’s how the spell works,” Twilight explained patiently. “The more ponies and people you have and the more they focus on their intention, the more powerful the portal becomes.”

She could see General Anderson already looking unimpressed, but he closed his eyes and began concentrating. Next to him, Blueblood and Sato both concentrated. Her friends all had their eyes closed as well, and Elliot too was concentrating. Even Hell Blazer had his eyes closed, an expression of scepticism on his face. Twilight turned to the empty field.

"Portus Maxima Liberatus!" she called out, concentrating as hard as she could on going to this world's Ponyville.

A bolt of white energy lashed out from her horn, seeming to impact on an invisible wall in mid-air before forming some sort of transparent doorway in mid air, through which a different place could be seen. At first the doorway was big enough to allow maybe a single person or pony through, but then it grew larger and wider as the spell continued to build, until it was large enough to accommodate dozens of people and machines at once. Through the portal, a small, almost deserted looking village could be seen - there were several shabby looking buildings that most of the assembled ponies didn't recognise.

“That’s Ponyville,” Twilight heard Blueblood say, the Unicorn Prince sounding almost confused. “But that’s…”

“Is this traversable?!” Anderson interrupted, sounding excited.

“I don’t know,” Twilight said honestly. “In theory…”

“Sod theory!” Hell Blazer said sharply, suddenly sounding angry. “We’ve spent years talking theory. It’s about bloody time we got some b - fucking results!”

Before anyone could stop him, the yellow Earth Pony walked up to the portal, a frown on his face. He reached slowly at the portal with a foreleg, before sticking his hoof through.

“Argh,” he said in a monotone voice. He pawed at a leaf that had fallen from a tree and pulled it back through the portal with him, before holding it up. “Ladies and gentlecolts - gentlemen even - I present an Equestrian leaf. Exactly as boring as the average Earth one.”

A moment later, Twilight released the portal and it quickly receded into nothing. The council, Elliot, Hell Blazer, the Doctor and her friends all looked at her, a range of emotions on their faces. Finally, Elliot spoke.

“Right then, everyone,” he said, looking around. “What’s the plan?”