Cloning is Magic

In the wondrous world of Equestria, a few friends gather from over great distances to discuss their lives and simply enjoy company. Daily they would gather and under the supervision of Princess Celestia's own hoof picked general, Gnr. Tej, they laughed and were happy.
One day, a new pony visited the group. A dark grey pony with a purple mane and tail called Daedelus. Slowly he became acquainted and was soon accepted readily into the community. Occasionally pulling a prank, such as poking somepony with a candy bar, he was no subject for suspicion. Until he bought the Rainbow Factory...
4 December.
Scale, the dragonpony of unknown origins, decides upon a nap in a tree in the everfree forest, the dangerous creatures having been killed by a gun squad formed by those in the land of Gnr. Tej, and was spotted by Daedelus. The pony knew now was the time to begin. He slowly climbed the tree and with bone saw in hoof, he snuck upon the innocent dragonpony. The vibrations caused Scale to awaken though and he saw Daedelus above him.
"Whaa.."
Daedelus spoke kindly after waking him up. "Greetings. My name is Daedelus, what is yours?"
"Scale. Who are you?" came the groggy reply.
"I lent you a saw at one point. I brought you a new one. One that is much... Much sharper" Daedelus' eves gleamed cruelly, his violet irises shrinking to pinpricks.
"I. I don't... I don't remember ever using a saw..." Scale began to stand up slowly.
"A pity then. Just look how sharp this is" Daedelus said, before swinging the flesh shearing blade at Scale's face.
Scale dodged and flew slightly backwards, not flying well due to his recent awakening. Again and again he doged the muscle tearing steel weapon and eventually missed a wing beat allowing Daedelus a clear shot at Scale's neck. One he didn't miss...
Scale awoke with a start and noticed a figure above him. A dark grey... Purple maned figure. He jumped into the air and flew into a higher branch.
"Stay back! Stay back you sick bastard!" Scale swore violently, terrified and hyped on adrenalin.
"Calm down! I mean you no harm! What is your name?" Daedelus managed over the dragonpony's ranting.
"What.. Where am I. Who are you. Don't kill me please!" Scale pleaded
"Calm down. I am Daedelus. I only wished to warn you of the storm." Scale noticed the dark grey clouds rolling in from the south. "Come, I shall buy you a sandwich. Dandelion and emerald would suit you if I am not mistaken."
"That... That's my favorite. How'd you know?" Scale inquired.
"Your body shape and colour tells all. You see..." Daedelus was interrupted by a sudden clap of thunder not all too quiet.
"Damn. I must be going. Here, go buy yourself that sandwich and enjoy your day" Daedelus said, leaving a rather hefty pile of bits in Scale's hoof
"Thank you Si.. Sir?" Scale looked around for the generous pony and left for the nearby town of Ynorb to buy his sandwich.
Daedelus walked on to a cave hidden behind a magical wall. Speaking his daughters name as his password, he entered and the sounds of crying ponies filled the air for a brief moment before being closed off by the granite wall again, the syringe filled with the dragonpony's blood in his saddlebags.

December 5.
The screams didn't stop and the colour coming from the Rainbow Factory was at an all time high, the blood of innocent ponies supercharging its production. Daedelus looked at the tiny stockpile of live ponies left and smiled, remembering his plan:
"I cannot take anymore ponies from Equestria without arousing suspicion. I need more energy though. I need ponies without lives. Without others who care for them. I need... Clones"
The dragonpony's blood proved useful in the early tests, showing the base genes neccesary for blood to be pumped and created in both dragons and ponies. But since dragons were slightly more... Unpredictable than ponies, he decided to create more pony clones. The only problem being the missing DNA as Scale's was running low. Then the local town of Ynorb came to mind. With his current standing there, he could collect enough DNA to create more than enough clones...
He took off his blood stained goggles and lab coat and washed himself before leaving for his new 'freinds'.

December 7.
The escape of two ponies into the Everfree was a major setback in Daedelus' plans. They not only knew the location of his lab, but also were still sane enough to remember everything. He spent an entire day hunting them and as careful as they were, they couldn't hide from him for long. He found them drinking from a fresh water spring and knocked them each out ,with a tranquilizer dart strong enough to kill a buffalo, in a small dose.
He made his way to town after a nights rest and brought with his supplies: Two syringes and a swab. These would prove more than sufficiant ,he decided, to collect the needed samples.
Once there, he greeted his friends Kaiden Phillipa, Frostburn, and the General herself. He also noticed a new pony, a shy purple coated pony with a soft green mane and purple wings.
"Hello madame." Daedelus said, "I don't believe I have made your acquaintance. My name is Daedelus. Might I ask yours?"
"Fillyshy. I haven't met you before, no. It's a pleasure to meet you." She said, barely looking at him.
"Please madame, the pleasure is all mine." Daedelus bowed and returned to the conversation between Kaiden Phillipa and Frostburn.
Soon thereafter, another friend decided to pay them a visit. Starlightbells. A colour changing alicorn from a distant galaxy. A long conversation ensued and Daedelus watched for any chance to collect his precious samples. This opportunity came when General Tej Stuck her tongue out at Kaiden. The swap was quickly removed, rubbed across her toungue and placed into its slot within Daedelus' saddlebags.
A strange glance was passed his way, but was shrugged off without incident. Fillyshy was attempting to converse with them but misunderstood a comment made and, in unnecessary fear, took off to the moon with her Pegasus wings powered by true terror. Upon landing there she was surprised to find that she could breathe, though narrowed it down to Luna having created an atmosphere while on the moon during her exile.
Daedelus took this opportunity as well and used a miniature teleporter to appear next to Fillyshy and pulled a syringe from his bags. Starlight knew this somehow and shot forth to the moon and tackled Daedelus, the syringe inches from Fillyshy's soft belly. Daedelus became enraged and stabbed Starlight where his target upon Fillyshy was.
Starlight stood wide eyed and looked sown at the 100ml syringe pulling the blood from her body. Daedelus twisted the blood sucking plastic tube and shook it violently, leaving Starlight with a gaping hole in her abdomen. Fillyshy screamed in horror and ran to her savior before reaching deep within herself and healing the wound.
Daedelus teleported the blood filled syringe and saliva coated cotton bud to the lab and lifted the empty one to aquire the last sample he needed. Starlight lept from the ground and using powers of immense proportion, she threw meteorites upon the evil pony, killing him instantly.
As the two mares on the moon smiled at each other they heard an evil cackle coming from the wreckage on the moon. Daedelus stood thereupon and launched as it it were a joke. Starlight flew and kicked him square in the jaw, knocking him to the ground.
Again the evil laugh emanated upon the moon and Fillyshy screamed as hundreds of Daedelus's surrounded her and Starlight. Starlight used her powers to teleport Fillyshy to the ground and struggled against her attackers. The Daedelus she kicked bucked in the tussle reached out to her and pulled a single hair from her coat. A hair form Fillyshy. The world grew black and she was suddenly covered in Daedelus.

Fillyshy ran to Ynorb and yelled out what she saw to Frostburn and Kaiden. Gnr Tej had left on official business and wouldn't return until for three more days.
Just then, the sound of machine guns firing flew through the air and grenades blew chunks of earth to the sky. The grenades were not standard ones though. The looked like... Rainbows.
Fillyshy saw the army first, but Frostburn and Kaiden soon saw it as well. A massive army of ponies. Ponies that looked like Daedelus, Tej, Starlight and Fillyshy's marched, aiming guns and rocket launchers at anything in front of them. The freinds quickly gathered any forces they could muster in twenty minutes from very close by towns and prepared to make a stand. The final stand against a clone army.

Starlight found herself bound on the moon, barely breathing and bruised from hoof to muzzle. The army of Daedelus' had beaten her to a pulp. Through sheer willpower alone she staggered to her hooves and made her way slowly back to Equestria. The pain almost unbeatable, her only thought of destroying the evil Daedelus himself.

Bombs, bullets and blood flew through the midday air as clone upon clone fell as Frostburn reloaded his AK47. Kaiden threw three more frag grenades and barely dodged a bullet aimed directly at his head. Clones kept pouring from a cave deep within the Everfree and with ammunition running low, it was only time before the army took the entire town. Fillyshy tended to the wounded, healing as quickly as possible but quickly becoming tired as a result. Unbeknownst to her, Daedelus himself was right behind her and teleported her to his lair as quickly as possible. Her power was indispensable and with only one hair, only one clone was created and her power was already depleting.
Daedelus did leave a small present behind though. A Rainbow-C4 charge of 20kg sat where Fillyshy's hooves were upon a wounded pony and the timer ticked slowly towards zero.

_
Daedelus pushed Fillyshy into a colour absorbing device, the blade moving slowly towards her heart and Daedelus smiling at the blood would give him the last part for his perfect clone army and the last needed for a Rainbow Nuke.
An alarm broke Daedelus' grin and Starlight staggered into the room, the bodies of thousands of clones lining the adjoining passageway. Daedelus smiled again and spoke.
"Well done. You arrived just in time to see the destruction of the resistance." Daedelus pointed towards a monitor above his head as the C4 ticked down.
00:03. 00:02. 00:01...
The screen went blank and a resounding boom shook the cave and the blood drained from Fillyshy's and Starlight's faces simultaneously. Daedelus laughed and a loud roar was heard not long after.

The C4 blew Kaiden halfway across the battlefield and Frostburn watched in horror as his friend's body flew limp across the sky. Eight massive tanks began to converge on his form and Frostburn flew into a rage.
He grabbed two belts of grenades, a repeating rocket launcher and ran, throwing the grenades this way and that with one hoof and firing the RL with the other. Frostburn knelt down beside the wounded Kaiden, roaring "No pony left behind!" Before pulling him to his hooves, throwing him over his shoulder and carrying him to the edge of the danger zone, explosions ringing all around them. Kaiden Phillipa pulled Frostburns light machine gun that hung at his flank and began to spray the weapon behind them, roaring.
Frostburn took cover behind a low wall, bullets whizzing past, and rested Phill against it, looking him over. He then took the gun, stood up and blasted it at his attackers, his throat becoming coarse from the roaring as he took multiple bullets to the chest. He then knelt down beside Phill, kissing him one last time before falling to the ground, having feinted of blood loss.
Kaiden Phillipa yelled in horror as he watched the life of his friend leave him. He began to punch and kick at the ground beneath him in a rage before pulling a grenade off of his side, standing up to face the oncoming walls of bullets, and then hurling the grenade through the sea of metal shells. Everything went super-slow-mo as the camera zoomed in on the grenade and circled it as all kinds of sprays of bullets missed or skimmed it before he fell through a smoke wall, exploding. Kaiden felt the rounds in his body, but the grenade and hit their assailants. He fell beside his only comrade...

Daedelus blocked the sloppy kicks and punches brought on by the tired and wounded Starlight and laughed at her pathetic attempts as he hit back harder and faster than should be possible. His attention elsewhere though, Fillyshy managed to slip out of the too loose buckles and grab the scalpel from the mechanical arm.
Starlight saw what was happening behind Daedelus and grinned. He stopped his onslaught and glared at her, only realising too late to stop the scalpel form being driven through his own heart.
Daedelus stood still in disbelief, his blood spilling from his chest onto Starlight and fell backwards. Fillyshy quickly healed her friend and watched as Starlight began to gather energy from all around her and blasted Daedelus into nothingness. A Daedelus in a large cage called them over and bagged the to kill him. Doing the same as before, she vaporized the stallion. A single note was left on the ground. It read:
"Thank you for ending the evil that my work has caused. My evil clone was too powerful. Destroy my lab, and please, tell my daughter I love her."
Starlight nodded to Fillyshy, signalling her ro leave as again she gathered the cosmic energy around her. She absorbed the corrupted energy of the Rainbow Factory and blew the entire mountain to nothingness, the work done by Daedelus destroyed and the remaining energy used to return the world to normal.

Kaiden and Frostburn awoke with a start and looked deeply into each others eyes, their feelings never again revealed, but always there.

Starlight looked across the barren plain that was once an evil lair, the rubble smoldering and the Rainbow Factory destroyed. Fillyshy reminded her of the note and Starlight wrote out in the afternoon stars:
"Your Daddy loves you."

The world reverted to normal and Daedelus' daughter looked up into the night sky in awe at the words written there. The destruction caused by Daedelus' work may have been reverted, but his work never lost completely.
*A young colt walks over the smoldering ashes and finds pieces of paper, miraculously unharmed, and compiles them with the same evil within him as that which possessed Daedelus*