Hello. Professor Paradox here. Before I let Mr. Smith continue with his story, some well needed context is required. You see, one problem with time anomalies, particularly ones that have only had limited experience in the three dimensional plane (as in recently leaving their temporal prison) is that they mainly see time as it pertains to them, rather than to the whole universe. To be frank, I had this exact problem myself back at Area 51. Regardless, what this means is that since Mr. Smith's main goal is to prevent further human experimentation, his view of spacetime is slanted towards that end.
Where things get complicated is when the lens of time for one's interests is in direct conflict with the natural progression of time itself. Nathan and that poor mare Pinkie Pie went back in time to prevent the Omnitrix from ever existing. With Nathan's warped perception of time, he thought this action would correct the timeline and prevent further experimentation on children. He couldn't have possibly known that the main purpose of the Omnitrix was to foster interstellar peace. He had never interacted with this technology before this intersection with his life in Equestria.
Now, some of you might remember that I am not allowed within 50 light years of any Celestial Sapiens, due to my proclivity to alter time itself. Regardless, they came to me after this incident livid at Nathan's alteration of time: "Paradox, it seems that this Smith boy altered time to prevent the Omnitrix from ever existing." One Sapien said to me. They elaborated: "The lad's motive is noble, he was a victim of experimentation and wants to prevent further anomalies, however that Tennyson boy is needed as a protector of the universe. We beseech you to correct this error, Paradox."
Well, I couldn't say no to the Celestial Sapiens. I mean, I value my life. So, I went back in time to 1096 CE on Earth, mere moments after Nathan and Pinkie Pie left and undid the damage. This allowed for all of the previous events in Ben's life to occur as they were supposed to.
Anyways, I provided this context lest you readers think that some sort of "Deus-Ex Machina" occurred in this saga. I may or may not be back in this tale, but keep your eyes peeled for any temporal anomalies :)
Woah, I don't get it. I erased the Omnitrix from the timeline. How in god's name is Ben here, as Alien X no less. Whatever, I don't have time to question this occurrence. I have two worlds to save, and Vilgax is probably on his way here to kill everyone.
"Smith, do the time thing. Bellicus and Serena (The two other personae inside Alien X) only gave me full control of Alien X for five minutes. I can hold him off, but not forever." Ben says.
I oblige, trying to render space in a manner that destabilizes Tirek's footing, altering the trajectory of his dark energy blasts. Ben creates five copies of himself as Alien X, and surrounds Tirek.
"Playtime's over, weirdo!" The five Bens say, as they open a black hole underneath Tirek's feet, sending him into the abyss. For anyone else, this would have been a surefire way to end the fight, but not Tirek. He jumped out of the black hole, closing it and decimating the four false copies of Ben to atoms.
"For a Celestial Sapien, you sure are weak! Are you sure you aren't holding back?" Tirek says, grabbing Alien X and hitting the green mark on its chest. This turned Ben back into a human.
"Ah, so you are a little Earthling boy, just like Project Eclipse. It's a shame I didn't use you in my experiments as well."
First mistake, Tirek. Don't bring up the experiments. "Ben, run. I know you can turn into aliens and stuff, but you need to run. Find my friends and run." Twilight said in a manner that wasn't typical to her. Ben had a feeling what Twilight was about to do, and rounded up the four remaining Elements and ran for the hills.
"Twilight, you alright? You seem off." I comment snidely. Usually, she doesn't have this kind of hesitation when speaking, let alone a raspy voice.
"I don't know what it is, but maybe Celestia was right. Maybe, you do have to shed blood to make peace." Twilight said with tears in her eyes.
"What? No! Don't fall in! If you kill, you will become addicted to it, and be no better than Celestia and Luna." I warn her, noticing that she is starting to lose faith in the power of friendship.
"Hmm, maybe we don't have to fight, after all, Nathan. I'll tell you what. I will make a bargain with you." Tirek says, using magic to encapsulate Ben and the four other ponies, holding them in the air for some unknown ransom.
"Queen Twilight, this impacts you as well, my dear. Pay attention." Tirek says with a smirk.
"In exchange for all of your alicorn magic, I will free your friends from this bubble. Obviously, I will conquer this planet and subjugate it mercilessly, but you have my word as a warrior that your lives, as well as these prisoners, will be spared.
Twilight was furious. All of her godlike power for ransom, in exchange for her friends? She can't even begin to comprehend the magnitude of this.
"I am not done just yet. As for you, Earthling boy. You killed my pupil Luna. Have you no pity for her? She gave you unimaginable power, and you did what with it? Abandon your creator, and kill her? So much for friendship." Tirek says, laughing.
"She fucking experimented on me, along with thousands of kids. That isn't right."
Tirek smiles: "Ahh, now is where things get interesting, my boy. Back in 1977, you stole something of mine. A floppy disk, I believe. That information contained my plans for Project Eclipse, in which you were the final product. That was only one piece of the puzzle."
What. What does that even mean? One piece of the puzzle? Is Tirek trying to play with my emotions?
"Go on." I say suspiciously.
"I want nothing of you anymore. Your battle in New York removed all of the weaponizations in you when Celestia "purified" you of Luna's influence. My work was done for naught. What I can do is give you vengeance."
"Don't listen to him, Nathan. He has some sort of plan to trick us. It is only going to hurt you in the end!" Twilight says. I want to listen to her. She is my friend, but I swore an oath to protect all children from experimentation.
I stare at Tirek stone-faced and continue to listen: "As you are probably aware by now, Vilgax and I were two of the founders of the Intergalactic Foundation, of which Earth was only one planet where these hybrid experiments were done. We did some of the grunt work, but we didn't come up with the idea."
Now I was intrigued: "Well, who did, wiseguy?" I say, eager to exact my revenge on whoever came up with the idea of human (or alien) experimentation.
"It was actually two people, if I recall. Sovereigns of a rogue state somewhere in the Andromeda galaxy. I can send you to that planet, and you can find and kill them. You want to protect the children, don't you?" Tirek says, eager to settle an eons long dispute with these people.
"Whatever you do, do not listen to him. I am begging you as my best friend. Do not, I repeat, do not do it. He will probably kill me once he zaps you to that planet."
I walk over to Twilight and give her a hug, the strongest hug I can give. "I am so sorry, but I need to do this. You can deal with this guy, but this is where our paths diverge. My mission isn't the magic of friendship, it never was. My mission was finding out who I am, and why I am. You can hate me for this, but I am accepting Tirek's offer. I need to find these bastards and kill them. I will always remember you for your kindness, and you will always be a friend to me. I am sorry."
Twilight was horrified: HER friend, the one who spent eons in frozen time teaching her the secrets of time and space, is going to accept a deal given by one of the people who made him a monster in the first place. "You...son of a bitch…" Twilight says, crying.
I walk over to Tirek: "I accept your proposition, on one condition. No matter whether Twilight accepts the second deal or not, her life WILL be spared. I demand it." I say, trying to make up for betraying my only friend.
"Done!" Tirek says, "In return, I ask that my life be spared as well. I was trapped in Tartarus during Luna's experimentation on you, and was only partially involved."
How many lives am I risking to get my revenge? It doesn't matter, I need to find these bastards and end them.
Tirek kneels and gives me his hand, which is glowing with magic, which I assume will send me to this planet.
"Do we have a deal, Smith?" Tirek says with glee. I accept his hand and firmly grasp it. "Deal!" I say, as my body gets enveloped in black energy and my body disintegrates, being sent away to a far away corner of the universe.
"NATHAN!!! WHAT IS WRONG WITH YOU!!!" Twilight says, crying. "I for one have integrity, and I will not accept your proposition." Twilight says as her once purple eyes began to turn blood red.
"This is quite odd, Queen Twilight. What is going on?" Tirek asks, puzzled:
"You probably killed him...my human...you killed him!" Twilight cries, charging up a massive attack. (Actually, Tirek didn't kill me, but Twilight was so obsessed with rage that she didn't care to think for a moment).
"Ah, so you fancied the human. Gross!" Tirek says.
"NO! Not like that you moron! He taught me what was important, and that friendship is overrated. Those poor ponies who don't know any better, and still think Friendship is Magic. I loved him like a brother, and you killed him!" Twilight sent a blast more powerful than anything she ever used before, with enough power of a thousand neutron stars.
"You idiot! By killing me, you killed all of your friends!" Tirek says, using Ben and the four other elements as human/pony shields. Twilight quickly pauses time, grabs the magical prison, and moves it out of harm's way. With the now resumed flow of time, this allowed for her neutron star blast to incinerate Tirek to dust and ashes.
The magical prison breaks, now that Tirek is dead, and Twilight breaks down in tears.
Fluttershy runs over to Twilight and hugs her: "Why did you kill him? He is evil, but he deserves to live." Fluttershy said naively, still believing that kindness is magical as well."
"Yeah, what the hay was that, sugarcube? You just burned the bastard to cinders!" Applejack said, appalled and horrified.
"My word, darling, you really went out for the count!" Rarity said, shocked that Twilight would kill.
"I didn't know Nathan that well, but that guy needs therapy." Ben says, while using his watch as a comms device to signal the Rust Bucket 3 to come pick him up and take him back to Bellwood, California.
Sadly, Twilight's worst fears came to pass. She really was just like her teacher Celestia. A bloodthirsty monster who could kill at a moment's notice.
UNKNOWN LOCATION: PRESENT DAY
I wake up on a military style cot. I have never seen this place before, and the environment is rather dreary and dull. I see a bunch of teenagers my age sparring in the arena across from me, separated by a thick glass wall.
"Glad to see you are awake, new guy." Says a voice I have never heard before. A young woman, maybe a year or two older than me, walks over to the cot. If I am not imagining things, she looks like a cat woman. I mean, I have met ponies before, so anything goes now.
My name is Force Captain Catra, and you are in the freight zone. Kyle found you floating in the vacuum of space two weeks ago. How a hominid can survive that is beyond me. We took you in, and you are in Etheria now. Your power levels are off the charts, so I thought bringing you into our unit would be a good idea.
Etheria? Power levels off the charts? New planets? Here we go again…. TO BE CONCLUDED IN A NEW FANFIC