At the end of the day, there is an undeniable problem with attempting to trap a reality warper, especially one capable of twisting space-time like a pretzel. Simply put, this is that it is basically impossible to contain them in such a way as to render their powers useless. Certain high-grade containment spells can accomplish this, but they require an absurd amount of magical energy to cast, roughly equal to the cumulative magic possessed by the average small town. Another method would be to deprive the reality warper of their magic, thus preventing them from using their abilities. Of course, in either case one would need to be capable of channelling almost absurd quantities of magic, and as Neuron Probe is not a Changeling Queen, nor a semi-immortal Centaur with a thirst for power, it can be safely assumed he did not have this ability.
Of course, reality warpers do have their own limitations, which prevent them from doing things like accidentally obliterating the universe with an ill-timed sneeze. But when it comes to something like removing their limbs from hastily-made, utterly mundane bindings in a cave, there is nothing, technically, that can get in their way.
The problem Pinkamena faced was that, in a manner of speaking, she wasn't a reality warper. She was too orderly and sensible to have the casual disregard for things like the laws of physics and common sense that all good reality warpers do. However, she still technically had the body of a reality warper; Pinkamena Diane Pie, better known simply as Pinkie Pie, had been a reality warper since birth. Her mind was shaped in the way that allowed her to take full advantage of her abilities, as was that of Surprise, the other personality sharing their collective brain.
Pinkamena was the only one of the three who could not look at the twisting fabric of reality and simply giggle. The experience was more likely to give her a blinding headache at the very least. Other possible reactions included things like dizziness and nausea. The latter problem, at least, had thankfully been slowly worn down by years of exposure to her more cheery counterpart's antics. But the tendency for blinding headaches still remained, and that was when she was watching in the 'passenger seat', so to speak. As for an attempt to twist reality personally? Trying to tear apart the foundation of the world because of its inconvenience, and force the world to accommodate her will? It was all but unthinkable. The last time she had done so, five years ago now, she had had a truly horrific headache as her mind tried to come to terms with the fact that she had seen and felt her leg stretch like rubber despite flesh and bone being completely unable of such a feat. It was all but impossible to hurt herself physically, what little instincts she had would see to that, but mentally it was a totally different story.
With this in mind, the fact that she was trying to figure out how Pinkie's teleport trick worked as quickly as she could said a lot about the situation.
Probe was only a few steps away from her now. Her heart was racing as she strained and pulled at her bindings, her panic threatening to overwhelm her as she desperately tried to escape. She had to escape, she had to! She needed to make a hole, a tunnel, from here to...anywhere, honestly. Sugarcube Corner would be great, but she could land on the other side of the cave and she'd be happy, just so long as she got away from him. And it would hurt, but maybe if she closed her eyes and ran as soon as she could then it wouldn't be so bad. Right?
Probe chuckled at her futile efforts, and finally stepped to within touching distance. The sharpened piece of metal, came closer. She could see now that it was not a true scalpel, more likely a piece of a can or something, flattened and shaped roughly with rocks until it gained the approximate shape. But it was still metal, still sharp, and coming closer!
She screamed, and finally pulled at something in blind terror. Something, despite being intangible, went 'pop'. Pinkamena
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l and hit the floor.
She saw it all, felt it all, with no disconnect between body and mind like when Pinkie and Surprise did it.
Probe looked into the hole in reality she had left behind.
This time, both Pinkamena and Neuron Probe screamed.
Halfway across the country in Manehatten, Discord jolted and gave a giant spit-take of lemonade, dropping the rest of his glass of cotton candy in the process. He whipped his head around and stared through the wall in the direction of Ponyville, thoroughly ignoring Luna's complaints of him getting lemonade all over her chess set. He had been confident that Laughter's bearer, given her abilities, would be able to protect herself from one deranged stallion, that he was free to tag along on the Princess's visit to the city and have some fun with her. That, obviously, was a mistake. He prepared to teleport-
Something was wrong. It hurt so much, things had twisted and shattered in front of her eyes that shouldn't have but they did and it hurt so much but somehow, Pinkamena still knew that something was wrong. She had made a mistake somewhere, hadn't done it right. And she had been wrong, it was so, so much worse than she had expected, she couldn't run like this, her head, her mind, it all hurt too much, she couldn't even see straight. She screamed and screamed and he screamed too, her pain and his terror mixing in the air as whatever was in the tear she had made fell away, fell away into the void between the atoms and the frames and the letters that had hurt so much to see-
And then she was out of the body and into the mind, shuddering and shaking, held in a comforting embrace even as she slipped into true unconsciousness.
The moment she emerged, her panic at Pinkamena's mistake overriding her fear of the doctor, Surprise wrenched reality back into place. Pinkamena's mistake had been simple in nature- it was too big a hole, and she'd forced it to stay open instead of closing naturally behind her. It was too unstable to last for long, but it had posed a risk to the immediate area. The rock they had been chained to was half gone as a result, torn away and flying through the gaps to who knew where. Hopefully it wouldn't hit someone.
Discord relaxed as the hole closed and snapped his claws, yanking the piece of rock back into reality proper. It flew into the room and, of course, landed right on top of Luna's just-magically-cleaned chess set, narrowly missing the mare's snout. Regrettable, but far better than it landing directly on some poor sap somewhere else.
He hastily began babbling an explanation before the irate mare got the idea to blast him with concussive magic.
The remaining Elements of Harmony and their accompanying guards barely felt a thing. The unicorns noticed the most, Twilight especially feeling the brief burst of wrongness coming from just up ahead. Something had happened.
'Hold on girls,' she thought desperately, blasting yet another golem into a tree, 'we're almost there!'
Probe had stopped screaming, probably from lack of breath, but he was still staring into the space Pinkamena had previously occupied. Surprise gulped, and began to slowly edge away.
Behind her, completely ignored until now, the small Timberwolf abruptly began to snarl and bark. Jumping, she whiled around, only to hastily dive to the side to avoid the young cub's pounce.
Unseen by Surprise, Probe twitched at the sudden noise and slowly turned around. In some ways he was actually lucky. Had he had a tighter grip on his sanity, his catatonia might have lasted months at the very least. But with his actual, far more tenuous grip on things, coupled with his growing single-minded obsession with a certain pink mare, he had actually managed to remain vaguely functional.
Of course, at this point he couldn't do things like reason, or think straight, or even remember what exactly he was trying to do in that cave. All he really new that he wanted the pink mare in front of him for...something, and that he was angry.
And so, instead of using his magic, which would have been a far more sensible decision, he simply let out a wordless scream of rage and charged.
Surprise, taken unawares, didn't have the time to turn around again before his shoulder slammed into her side, sending her sprawling. She gave a pained gasp at the impact, the pain settling into ribs. That was going to bruise for sure. Nothing was probably broken though- it took more than that to break the bones of an Earth Pony.
Probe dashed forward and reared up unsteadily, clearly aiming to slam his hooves into her as hard as he could. As he came down, she bucked out with a hind leg. He took the hit with an audible 'Oof' and fell to the side, missing her. His legs half-collapsed under him as they struck the unforgiving stone floor, and he let out another yell, half angry, half pained.
Now the Timberwolf howled, and ran in, patience expended. It pounced and she rolled awkwardly to one side. An outstretched paw clipped her side, scratching three long lines into her skin. The Timberwolf's momentum carried it across the floor, and it landed with a wooden clatter as she scrambled to her hooves.
Probe, thinking slightly clearer now, tried to conjure a rope to bind her. The magical lasso barely tightened around her chest before she turned her body fluid, allowing it to slip through the loop as she merely cantered forwards. She ducked under the Timberwolf's second pounce and dodged telekinetically-hurled rocks to the beat of a twitching tail.
Next, Probe grabbed her, lifting her into the air, but his magical grip was too weak to hold her for more that a few moments. Surprise dropped, and this time had to pull a hind-leg out of the Timberwolf's closing jaw, drawing fresh blood as it grated against the young monster's teeth. She gasped in pain and landed awkwardly, on her hooves but only just. Her leg gave a painful throb as she put weight on it. Probe darted in, and she dove to one side, but her injured leg protested and trailed behind. Probe tripped over it, and the impact sent both of them to the floor. Surprise bounced with the impact, and ended up against the cave wall.
Surprise breathed heavily, trying to catch her breath even as Probe struggled to his hooves, somehow still finding the strength to carry on. He limped towards her, horn lighting up. The uncomfortably familiar sight of the makeshift scalpel came floating back through the air towards him as he advanced. By now, his face was a mask of fury, all other thoughts and feelings having long since departed his mind. Considering that it was probably more than a little broken by Pinkamena's warp, some part of her quietly realised, feeling angry might be all Probe's mind was actually capable of at the moment. The Timberwolf, growling lowly, was slowly circling them both.
She recognised this scene. She had seen it, on rare occasions, when carnivorous animals chased their prey onto the family farm. It was the part just before the pack leader killed its prey. Icy fear flooded her at the thought.
"NononoNONONO!"
And before Surprise could do anything more, Pinkie Pie finally retook control of her body.
Pinkamena had knocked herself unconscious trying to escape. Surprise's desperate fight had left her battered and injured. The monster walking towards them had hurt and terrorised them all in the present, in the past, and in uncountable nightmares in-between. Neuron Probe had, bluntly put, been a blight on her life for nearly as long as she could remember. She was scared, terrified even, but more than that now she was increasingly angry, and sick and tired of the whole bucking mess. Pinkie rolled onto her back, braced herself against the gave wall, and met Probe's eyes.
"I'm tired of being scared of you," she told the deranged stallion. She doubted he really understood her, but it felt good to say the words none the less. Probes only reaction to the sudden change in demeanour and defiant words was to snarl, come closer quicker-
Pinkie bucked him in the chest with every last scrap of natural strength she had. Probe went flying across the cave, the Timberwolf watching him arc over its head. He hit the opposite wall, and crumpled to the floor. In the moment of silence that followed, Pinkie heard the low echo of slightly ragged breathing separate to her own, and relaxed. He was unconscious.
Her attention returned to the TImberwolf as it howled, angrily. She watched it, tired and almost disinterested and it made to leap. As it's paws left the ground, she began to tug herself back to her bedroom in Sugarcube Corner.
"PINKIE!!"
Abruptly, a bolt of crackling purple energy crashed into the Timberwolf's chest, colliding with some sort of metal construction there that had a gem embedded in it. The gemstone reacted with its own pulse of bright energy, and the Timberwolf disintegrated in mid air- its various pieces flung in all directions by the force of the magical explosion.
Pinkie blinked, and looked towards the cave entrance, releasing her grip on space-time. Sure enough, Twilight Sparkle stood there, breathing heavily, obviously half-exhausted by the journey there.
Pinkie raised a hoof and gave Twilight a tired wave, matching it with an equally tired, but content smile. "Heya Twilight. You should see the other guy."
There was a pause as Twilight gave her a look, before running towards her into the cave, a relieved smile on her face. Behind her, their other friends appeared, along with a lot of guards. "No, seriously, you need to tie him up before he wakes up, I think he's even nuttier than he was to start with now, with the whole living in a cave thing and all the warping. Oh, and a lot more hurt."
She would have said more, but by that point she was too busy being hugged by her friends (and then forgiving them for squeezing one injury or another) to really consider doing anything else for a while. At least there were guards taking care of Probe.
Eventually, they broke away, and helped her to her hooves. "Let's get y'all home," said Applejack.
"I can't wait! It's like it's been years!" smiled Pinkie happily.
The moment was unfortunately then somewhat ruined by Twilight demanding a visit to the hospital instead, but Pinkie just gave a tired giggle and nodded her head in agreement. It didn't really matter, after all. She was safe.