Project Omega

"Tell me how you did it." the purple, alicorn interrogator said brushing a strand of her mane from her face .

"Wouldn't you like to know." the prisoner responded, not lifting his head off the table.

"Why do you have to be so infuriating? Tell me what happened between you and him." she said.

The man paused before saying; "What are you after? The rest were Equestrian Intelligence. But you're something different." the prisoner responded.

"This isn't about me. We want to know how you became like this and how he didn't. How you beat them and almost destroyed Equestria!" she rebuked.

The human lifted his head off of the table and looked at the mare. His eyes were... glowing. Glowing a bright red and leaking a smoke-like aura. "No... No you don't." he said calmly. "No one should repeat my life, just to become like me."

"And what exactly have you become?" the mare asked, now intrigued.

"A monster." he said. As those words lefts his lips a swirling portal opened up behind him, sending purple lightning around the white tiled room. His shackles, restricting him to the table, disappeared off his wrists in a bright flash. He got off his chair and walked to the edge of the swirling portal. "See you yesterday.", he said with a smirk as he stepped into the portal, immersing himself in the vortex that disappeared in a white flash, leaving a scorch mark on the wall.

The interrogator was left in a white room, with a a black scorch mark on the wall, a smile plastered on her face. 'Well,' she thought to herself, 'We better wake up Atlas before he gets pissy.'

In the Royal Canterlot Bedchambers

Celestia awoke to a swirling vortex, shooting lightning, opening in her bedroom. Readying her magic, she prepared for the worst. Discord. Sombra... Chrysalis? Instead, a small six foot frame stepped through, a few inches shorter than her. She recognized him instantly.

Chronos

"Hello ole' girl." he started nonchalantly, "Wondering when you'd see me again?"

"No... I suppose not. No cage can hold you forever." she replied after a moment's hesitation. This man, was responsible for countless deaths. Ponies, gryphons, dragons, all fell before him. And even he openly admitted that the only reason he didn't destroy her was she was fun to tease. This was a truly insane being.

She was about to call the guards when she felt his magic surge and cut off any sound from exiting the room. His magic was always different, not conforming to the laws and theories of magic, but to him. She closed her mouth with a "hmph" to voice her distaste for the man.

"Now, now," he began, "I just want to talk."

"And what, prey tell, would said chat be about?" she asked with a little venom.

"Well, when I came here, you completely fucked me and him in the ass with the shittiness of politics and twisted us around your finger."

"Get to the point."

"I," he began slowly, "want to remove that and just bring out the good in us that you always wanted. And in return, full amnesty."

Celestia pondered this for what seemed like hours thinking about the pros and cons. If she let him go, she would have the worst criminal in the history of Equestria on the loose. Although if she didn't let him, she would still have this war crime trial to hold with the gryphons.

"Fine." she finally said, leaving a bad taste in her mouth.

And one of the man's signature smiles become plastered across his face.

"Thy will be done, princess." he said sarcastically with a shallow bow.

5 Years Earlier

"Subject Atlas is in range. Permission to execute phase one of Project Omega?", a masculine voice came over an enchanted mirror.

"Proceed." was the response in the mirror, this time from an elegant, feminine voice.

"Affirmative." the operative said in response, a smirk on his face. He readied his magic, knowing that he would need a great amount for this human in particular. The other one had used most of his magic already, but thankfully the princess had given him various charging crystals. And with no pure nodes around here, he was tough out of luck if he ran out of magic too quickly.

"Time to meet the newby.", he chuckled.

//O\

"So you're not coming over tomorrow?", a boy around the age of thirteen asked over a phone.

"Naw, man. I got drafted into working with my grandpa.", a voice came over the phone of a boy relatively the same age as the other and a slightly accented.

"Well crap man. I already got the stuff out."

"Sorry. But what can I do?", he replied. The call remained silent for as the boys remained silent to think of something to say, but a faint sound was heard on the accented child's side. "Aw, crap. I got it mom!", the boy shouted over the phone which got the first one to chuckle at his friend's remark.

"Someone's at the door. See ya' on Monday Sam.", he said as he hung the phone up.

Sam sighed in annoyance, knowing he wouldn't see his friend for the weekend. Which was kinda bad. The uh... stuff he mentioned, yeah that was kinda important. You see, Sam and his long-time friend, Gunnar, just found out they had, well... magic. It started out simple enough, a few floating pencils, a few lifted skirts here and there. Nothing too big.

Now, this weekend, they were actually going to test the extent of their powers. These tests included a few weights of assorted weights to test strength, a gallon jug of water to test dexterity, and a brand new chronograph to clock the speeds at which they could hurl objects.

And all this preparation for nothing. Although Sam could do these tests alone, it wasn't the same. No sense of competition, and just not having him here would put the mood off.

Lost in his thoughts, Sam almost didn't here the knock on the door. 'Strange.' was all came to mind in his head when he heard the sound, since he lived pretty far out in the country. He got off his place on the couch, instantly regretting it since it was pretty cold in his house. Walking to the door, he tried to look through the glass inlay next to the door. All he could see was a dark figure standing in the evening sunlight.

'Great, a freaking creeper.' he thought as he remembered the handgun next to the door his dad always kept. He made a mental note of this as he always had. Blame it on a small phobia. He was home alone, isolated, and a stranger walks up to the door. Good reason to be paranoid.

Twisting the doorknob he kept one eye on the gun's compartment as he looked to the strange man. He was in a dark trench coat, which had several bulges protruding out like he was wearing something underneath. His face had several scars, red hair identical to his own, and bright blue eyes. Before the young man could speak he was interrupted by a sinister smile across the stranger's face.

"Why hello. I've been looking for you newbie."