She Never Stopped
Twilight settled back on her haunches and dusted her hooves off. The spell emitters were aligned correctly. It had taken her a few years of off and on research, but she had finally cracked the spell matrix a few months ago. It would still require an Alicon's unique harmonic magic signature. Even if ponies of the three tribes somehow extracted their own magic, the blending required was impossible by current artificial means.
She cast a wary glance behind her at the subtly vibrating spell battery. A containable source of chaos magic had been much more difficult to obtain. Discord wasn't playing nice this decade, not that she wanted him knowing what she was doing in the first place. His stance had never softened, hypocritical as it was. If not for the difficulties it created for her, she'd almost call his absence a blessing. Even after all this time he wouldn't support this.
Levitating a cord over, she clamped the feed wire into the battery, glancing over at the instrument board to watch the array saturate.
Taking a seat, she lowered the thaumic capture rig over her head, settling it snugly around her horn. She channelled a spark of her magic, watching the readouts as it mixed.
100 years of quiet research. First with Starlight, then with a succession of the brightest magical and technological scholars of their day. Her own faithful students. Every one pushing the boundaries of magical knowledge, pushing forward the progress of the pony race and Equis beyond.
The teleportation relay could be laid at the hooves of her students. Shields capable of withstanding the pressures of the ocean floor. Medical research saving countless lives. The depths of magical theory had been delved, horizons expanded. A worthy pursuit, the goal the betterment of all.
But in all things there was a quiet motivation. How does this magic interact? Could this matrix be deciphered? Ten thousand innocuous little questions over the course of a century. All leading to this moment.
Flurry was indifferent, Cadence cautiously in favor. The sisters were against it, but they had passed their authority down to her. Then made the unilateral decision that created this situation in the first place.
Twilight fought the urge to grind her teeth, instead focusing her efforts on pushing more of that unique Alicorn magic into the array. She'd spent weeks preparing precautions. If the worst happened, a shield array would snap down over the entire cavern, fed power by a stockpile of spell batteries. Not even she could penetrate it from the inside.
It would never come to that. Their spears had been blunted in the course of Twilight's research. 100 years of progress, and the smartest minds of three generations, had rendered them unto children.
Twilight winced, the flow of her magic almost stuttering out. A sharp breath and narrowed eyes accompanied the steadying of the stream. There was no room for mistakes now.
Steeling herself, Twilight cut off her magic, flicking a switch with her hoof as she levitated the capture rig back to it's podium. If anything were to go wrong it would be now, as the chaos magic mixed with her own.
The runes etched painstakingly into gems placed throughout the array did their work however. Reactions were dampened, bare metal taking on a pearlescent shimmer. Letting out a breath she barely knew she'd been holding, Twilight stepped forward to the main control board of the array.
This would perhaps be the most intricate casting to have graced the face of Equis. A counterspell to the combined might of the three most powerful beings on the sphere, meant to last forever.
Done in secret, in a rough cave a mile beneath the edge of the Everfree forest.
It had to be done. Twilight wouldn't let this hang like an executioner's blade over the neck of a bright future. She might not have created this problem, but as the ruler of Equestria it was her responsibility to Resolve it. Not tuck it away or put it on display as some object lesson.
Despite the example, villains still reared up. Ambition would always flare. Misplaced justice would lead to tragedy. There was no perfect world, and Twilight's charge was not to make it so. She was charged to spread understanding, and with that the friendship that could blossom in the absence of fear.
Twilight's hoof came down. Gems flashed. The hum of magic became a roar as beams shot out, refracting and twisting in preset fields to create a layered lens of spell matrices. The primary focus gem discharged, pushing power through said lens to battle with the will of gods made manifest.
There was nothing gradual in her spell's effect. Stone vanished, replaced by flesh. A crimson shield that was none of her doing snapped into effect, sharp hooves cracking against stone and a buzzing filling the air in a flurry of obscured movement.
Twilight simply waited, noting an emaciated silhouette stand firm in front of a huddled figure behind it. The only sound was a murmuring too quiet to make out.
Eventually the shield dropped. Tirek's arms lowered while his eyes burned into hers. Without a word, he turned to lay a hand on Chrysalis' shoulder, looking down at the mostly still form clutched between her forelegs. He lowered to his knees, free hand settling in a curly mane as a sibilant voice crooned gently. Following his gaze, Twilight hung her head and sighed. She'd always known in her heart of hearts that she would be too late.
"You won, Princess. We won't fight you." Chrysalis shuddered. "An effective lesson in empathy, comforting a child as her mind slowly unravels."
Cozy Glow's wide eyes stared vacantly at the ceiling, her face locked in a rictus of fear as her wings twitched feebly. Her chest rose and fell achingly slowly... Twilight stepped forward, eyes misting as she finally caught the murmur's meaning.
"I'll be good. I'll be good. I'll be good..."
Author's Note
This one really needed more room to breathe 
