Gallopfry was now indestructible. At least in theory. In reality, that turned out to be the overly optimistic sales pitch of a time bubble salesman. Technically, he wasn't wrong. Nothing could destroy Gallopfry now. However, nothing could get in either. Or out. Ever.
You see, it turns out that surrounding something in a time bubble for all of eternity is basically the same as destroying it. And when you trap an ancient society whose only pastime was time traveling and watching other civilizations in a time bubble forever…
Let's just say that claustrophobia, boredom, and time machines are never a good combination, and the moment the time bubble was activated, Gallopfry blinked out of existence in every spot of time and space.
The good news was that a handful of its residents, Time Lords, were out and about time traveling during all of this, and because of that were spared from the debacle. The bad news was that all but two were eaten by a sentient pan dimensional astroid thing. The worse news was that these two were the most psychotic lunatics produced by Gallopfry.
One occupied his spare time by traveling to distant worlds, bringing death and chaos in his wake, then saving innocent people until their gratefulness alone could keep him alive. The other one was the Doctor, who occupied his spare time trying to convince himself that wasn't what he was doing. The Doctor and the Master, the two remaining Time Lords, thus often clashed.
After foiling the the Master's diabolical plans yet again, and finally just caving and giving him a planet he could do whatever he wanted with, the Doctor was milling around time and space wondering what to do. After a good amount of consideration and bad amount of brooding, the Doctor chose to take the Master's advice and take a mentally handicapped companion, because, I quote, "they'll be impressed by anything."
Immediately he remembered Derpy and took her on his grand tour of time and space.
Nothing interesting happened whatsoever, until one day when he took her to a remote planet remarkable only for its repeated failure to make first contact, and thus, was the third most boring planet in the galaxy.
"Welcome," he said, with a dramatic flourish, "to Equestria. Circa 2013."
Derpy looked at the paleolithic landscape in confusion. "2013?"
"Relative to last world we were on."
Derpy got the joke, but smiled and blankly nodded anyways because the Doctor got depressed when he found out people could understand him. In reality she was perfectly intelligent, but a childhood with horrible eyesight and worse teachers created a huge gap between her and the normal pony. A month with the Doctor had all but removed that gap, though, a fact she desperately tried to hide because of a nagging suspicion he was specifically looking for someone mentally handicapped as a companion. "So, what's on this world?" she asked, with as much blankness as she could muster.
"Stuff."
"Stuff?"
"Cool stuff."
"Cool stuff?"
The Doctor snapped his hooves. "You said it."
Derpy was unimpressed. "It can't be too cool. It looks like my old home."
"You mean… you didn't grow up on that space station?"
Derpy looked offended. "Of course not!"
"How did you get out there, then?"
"I hitchhiked."
The Doctor gaped. "You what?"
"I got a ride."
"That's impossible."
"Why?"
The Doctor thought of a couple different reasons, then settled on one very important one. "I thought I was the only person that gave hitchhikers rides through space."
"Well… no."
The Doctor tried to wrap his head around that. Eventually he gave up and just said, "Right."
They then sat there for five minutes and stared at nothing happening.
"You sure take me to a lot of boring places," Derpy said.
"There's a reason for that," the Doctor said. "You want to know what happened when I went to exciting places?"
"What?"
"People died."
"Come on," the adrenaline deprived Derpy said. "Not everyone died."
"The universe compensated with cruelty."
"Cruelty?"
"Have I told you about Clara?"
"Who?"
"She was with me for about a week."
"And?"
"She ended up dying about 2 billion times across all of time and space."
Derpy winced. "Ouch."
"You said it. And have I mentioned Rose?"
"No."
"Well, she got stuck in a parallel universe with a clone of me."
Derpy looked confused. "That doesn't sound bad."
"A clone of me that's not a Time Lord and has a slow growing TARDIS piece. So, bored, dying, claustrophobic, and going to have a time machine soon."
"Oh." Derpy thought about it. "Why would you give a growing TARDIS piece to someone like that?"
"I didn't. Another clone did."
"What?"
"Now her brain is fried, and if she remembers any of it her head will explode."
"What?"
"And then there's—"
"Just stop," Derpy said. She was at least intelligent enough to know sitting through the Doctor's exes was bad for her jealousy and her stomach. "I get the idea."
"Okay," the Doctor said, and they stared at the landscape a bit more. It lost novelty with each passing second.
"I'm going to take a walk," Derpy said, tired of the awkwardness.
"Okay. Don't go too far."
Now, you see, the funny thing about rewriting history is that it's not nearly as dangerous as any time traveler makes it out to be. Any seasoned time traveler will tell you messing with your own timeline will cause the universe to explode, giant space meatballs to come and eat everything, or some other gruesome ending. This is simply not true. In reality, the universe is surprisingly good at compensating for timeline issues. The problem is the headaches that inevitably causes. Often, the way the universe compensates is so complicated and paradoxical just thinking about it is good enough to cause a migraine, to the point where some time travelers wish their changes would cause the universe to explode simply because that would be easier to understand. Thus, it's become an unspoken rule among time travelers to tell companions that messing with your own timeline is a bad idea, and bribe some space meatballs to gruesomely eat things once in a while to emphasize the point, because it's the only thing that will make others approach the issue with due caution.
This is relevant because if the change is big enough, the headache starts retroactively, which was currently happening to the Doctor.
"Argh!" he groaned, clutching his head.
Derpy, now a good 3 yards away, looked back. "Are you okay?"
"Yeah, I'm fine," the Doctor said, but continued his unsightly grimacing.
"You sure?" Derpy said, rushing back. "Maybe you're sick."
"No, please, don't—"
Then the headache exploded into a full on migraine and the Doctor collapsed to the ground in agony.
"Doctor!" Derpy yelled, and flew to his side. "What's wrong!?"
"It's… it's just a migraine… a really bad migraine…" the Doctor said. "This usually only happens when…" He looked up to Derpy. "Did you step on anything right now?"
"What?"
"Check your feet. Now!"
Derpy obeyed. On the bottom of one of her hooves there was a dead butterfly.
"The butterfly effect," the Doctor said with no small amount of horror.
"The what? What's the butterfly effect?"
"It's a time traveler's worst nightmare," the Doctor said. "Time is always in different states of flux. There are fixed points that will happen the same way no matter what you do in the past. There are slightly fixed points that will happen slightly differently. And then there are loose points, where the alteration of the path of a single butterfly in the past will completely change a world's history."
Derpy looked at the butterfly in shock.
"We need to get back to the TARDIS now," the Doctor said, struggling to stand up. "We need to see how much history is changed."
The Doctor, forgetting his migraine in the adrenaline rush, ran back to the TARDIS at full speed. Derpy flew behind. Once there he unlocked the TARDIS, burst open the door, and immediately started fiddling with a computer console.
"What are you doing?" Derpy said. She knew explaining things would keep his spirits up.
"Checking the TARDIS' repository of known history. It's protected against timeline changes, within reason, of course," the Doctor said. Derpy knew this was serious because he didn't explain how. "Let's see… it looks like the civilization on this world stays fairly consistent. Some places urbanize, but most of the planet sticks to a fairly agricultural lifestyle. But eventually…" The screen started filling with static. "Dammit! Just how big of a change did this cause!?"
"I'm sorry," Derpy said, throwing the dead butterfly on the floor. "If I hadn't—"
"It's no use blaming yourself," the Doctor said, grabbing Derpy. "If the timeline here was this fragile anything could've disrupted it. If it wasn't you, it would've been someone else. It's not your fault, okay?"
"Doctor…"
"It's okay."
"Doctor, behind you!"
The Doctor turned around to see, through a static filled image, himself on the monitor.
"This is yourself from the future," the monitor screeched. "Leave this world now, while you can. You have minutes at the most. This world is sealing off."
"What!?" the Doctor yelled in terror and confusion. "What do I mean, sealing off!?"
A different, more desperate Doctor appeared on the monitor.
"Do it! Leave! It's the only way to prevent this world from complete destruction!"
Yet another appeared.
"Whatever you do, do not help the princesses!"
Another.
"Run! This is your only chance!"
The screen started to be bombarded with different variations of the Doctor, some regenerated, some not, all in some stage of panic. He could only catch part of each message.
"—gods—"
"—monsters—"
"—endless cycle of destruction—"
"—the weapon—"
"—universe itself balancing it out—"
"What's going on!?" Derpy yelled.
"Whatever happened is so large, the universe can't change it all at once! It's leaving the walls between timelines open for a bit!" the Doctor said. "We're getting every single message I could possibly decide to send in the future at once! And if I'm right…" He paused. "Every single timeline in this world drives me to send a message to the past out of desperation."
Derpy grabbed the Doctor by the shoulders violently. "Then listen to yourself! Get out!"
The Doctor stared at Derpy for a bit, amazed, then rushed over the controls. But right when he was about to turn the first lever, the screen stopped with one final message, noticeably calmer and more articulated than the others.
"If you're hearing this," the future Doctor said, "it's too late. You've chosen to stay. Again."
The Doctor stopped.
"Don't try to leave. I say that because it's the only way to guarantee you'll try. It's important you know your situation."
The message ended. The Doctor went back to turning on the TARDIS.
"Don't bother," Derpy said, sitting on the ground with no strength. "It's too late."
"I have to try!" the Doctor yelled.
"No," Derpy said, "that's not what I meant. It's too late for me."
"What? What are you talking about!?"
"I wasn't in any of those messages."
The Doctor stopped and looked at Derpy. "I'm sure nothing happens to you."
"Don't lie to me!"
"If I have to send a message to the past this time, I'll use you."
"What we just saw is proof that never happens!"
"Still," the Doctor said, "I have to try." He flipped one final lever, and the TARDIS went careening off of the planet. "Open the door! Tell me what you see!"
Derpy ran and opened the front door. "I can see the planet we're leaving. We're passing a couple more planets. An asteroid belt. And now…" Derpy stopped. "Nothing."
"Nothing?"
"Nothing. Absolutely nothing."
The Doctor checked some readings, then slowly headed to the door and stood next to Derpy. They both looked outside and saw nothing but darkness. No galaxies. No stars. Nothing except a speck in distance. That solar system.
"What happened?" Derpy said. She clung to the Doctor. "Did the entire universe get destroyed? From that one butterfly?"
"No," the Doctor said, "but the real answer isn't much better."
"Tell me."
"We're in a time bubble."
Derpy's eyes widened. "Isn't that what—?"
"Destroyed my home planet? Yes. There's no escape. No way in or out. The only way out is to try to change the timeline so you never get trapped, which as you noticed, rarely works." The Doctor looked down. "We're stuck here now."
Derpy was silent.
"The only person in this sector that knows how to make a time bubble is me. The only reason I would create a time bubble is whatever change that butterfly unleashed created something so horrible I was willing to trap myself to keep it from reaching the rest of the universe. That probably means it's something intelligent. Something that outmaneuvered me repeatedly." The Doctor paused. "That cannot be good."
Derpy looked at the Doctor. "Does mean that we'll have to make that time bubble later?"
"Not necessarily. Time bubbles affect multiple timelines at once. If I get that desperate in one timeline, it affects them all. That's why they're so effective. As soon as you've created one, it's always existed, at every point of space and time. And because of that, they're extremely secret. Only three people in universe know how to make them, and they're all me."
"What?"
The Doctor shrugged. "Timey-wimey."
Derpy giggled a bit, but stopped when she saw the Doctor's face.
"But that's not what's scares me about this," he said. "What scares me about this is how big this time bubble is. I put an entire solar system in a time bubble. That takes, literally, unthinkable amounts of energy. Just putting one small planet, Gallopfry, in a time bubble meant exploding every star in an uninhabited galaxy. I don't even know how I did this. I mean, I hope I didn't explode 10 galaxies to do this, but if I did I must've had a good reason. And that's what really scares me, because I can really only think of two reasons I'd go to that much effort."
"Two?"
"One, that whatever that change unleashed is that big."
Derpy shuddered.
"I doubt that," the Doctor said. "Big is fine. I can deal with big. It's, unfortunately, probably the second reason."
"Which is?"
"I didn't want it to get bored."