Discord gained a very good distance from the the reptile he then stopped and glanced at his hostage. "Now whats a filly like you doing with those strange looking ponies and what can you tell me about your lizard friend?"
The little filly stared at him before she answered. "I'm not suppose to tell anyone. The grown ups say me and my friends are special secrets."
"Secrets? Friends? There are more of you?"
Before the pony could answer 682 suddenly arrived and stopped his teeth baring and steam was coming out of his nostrils. "Let. Her. Go. Or you'll be sorry in more ways than one."
"Oh but that's no fun, how about you tell me what makes this little girl and you so special?"
"Hurt her and you'll find out..."
Discord used his other claw which started to emit electricity. "If you insist..."
But as his electrifying claw was about to make contact with her body it stopped only for Discord to suddenly feel something in his chest. He then dropped the filly who managed to be caught by her friends maw. Discord was soon on the ground clutching his chest in pain. "What is this? What's happening? What did she do to me?!"
The filly ran and climbed on to 682's back. "She didn't do anything. She didn't have to. What you experienced was what happens to anyone who threatens her. So Discord you have your options, restore or there will be even bigger consequences."
"Over my dead mismatched body" he grunted as he still clutched his chest.
"That can be arranged." He said as he then roared in his face. All discord could do was look at his teeth in fear.
==============
Meanwhile outside of town the injured soldiers and scientists were still being tended to but then suddenly they saw a bright flash that began to consume Ponyville. Within seconds it dies to reveal Ponyville back to normal along with the clouds back to being white and fluffy. The soldiers in black wasted no time in charging into town. Agent Sweetie drops followed behind with a box. They soon arrived in the town square to a sight.
There was Discord lying on his back with what looked like multiple bite marks and claw marks all over his body. One of his horns was snapped off and one of his wings lost all it's feathers. He was a quivering scared wreck. The soldiers wasted no time tranquilizing him and making sure he was taken away.
SCPs 682 and 053 were nearby. Sweetie Drops approached them and placed the box in front of 053. "Here you go sweetheart your other friends want to see you're ok."
Out of the box came a little colorful teddy bear with heart shaped patch on him as well as a wooden toy train that moved by itself. The little filly giggled as she began playing with them. The bear climbed on her back and rode her as she chased the little train. Sweetie Drops then turned to the hard to kill reptile. "Amazing work out here. I knew it was a wise decision to use you."
"The child helped weaken him a little. What happens now?”
"I managed to strike up a deal. If all goes well, we'll consider giving you a place of your own to stay outside the facility. Particularly a swamp within the Everfree Forest. And don't worry we'll organize trips for 053 to come and visit." Explained Sweetie.
The beast nodded in understanding as the soldiers took Discord's unconscious body away in chains. Just then six mares walked up. "What is going on here? What happened to Discord? And what in Celestia's name is that?" asked Twilight pointing to 682.
Sweetie Drops pulled out a device. 682 just closed his eyes in anticipation. The filly and the toys were already far enough. A bright flash came and the six mares were in some sort of trance. Agent sweetie drops cleared her throat. "You managed to subdue Discord with the elements however he was taken away to a place where his petrified form will never be free again. Equestria is forever grateful."
The mares were still in a trance as 682 cleared out of the area and back to the outskirts of town. Agent Sweetie Drops followed taking notice of the other agents giving anesthetics to other ponies who saw the fight. What happened here may have been chaotic but some secrets are still meant to be kept. For now at least.