● Years Later,
6 Years into the Equestrian Space age.

The Rift, an air pocket in space. An entire asteroid belt with good old diluted Oxygen. Most of the Asteroids had been chiselled into islands. Then given a stronger, Earth Norm, field of gravity despite most being only big enough for a large building, yet the moment you step off the island you float through the void with just enough gravity to steer. This whole place was teeming with magic. As it should, for it was constructed, by a civilization of sentient animals called "Yokai". They constructed this place to escape the harsh nature of their own dimension. The Yokai had settled this belt 10s of thousands of years ago, meaning most of it was converted to their needs.

For centuries they used it as a port, using portals they constructed to travel to every habitable planet in the system. Now, with the native species able to travel through the solar system and all the worlds of it terraformed for each species, the Rift had become the center of trade for the system. It just made sense. The Yokai built each city (not just major cities) their own portal to the largest island in their system. That place looked much like a 21st century Earth Airport... only the gates were portals to other worlds. Yokai were masters of inter dimensional travel so setting up links to places in the same universe were easy. This made it faster to just come here before going to another city (even the ones on the same planet).

Once the ponies found this place and negotiated proper trade and travel rights, the Rift flourished. The Yokai even began allowing other civilians to build on their floating Islands. A proper space dock was even constructed at the edge of the air bubble, to promote themselves as the center of trade for even the larger shipments between planets.

Eventually, within the past year, the Rift became where all the planetary governments of the system gathered together and discussed system wide laws. Each world had their own independence well agreeing to obey the laws of the system. Even establishing the Inter Planetary Fleet to protect all worlds.

Equestria had only lead their world into the stars 6 years ago and had accomplished so much with hardly a conflict. Of course terraforming all the planets and giving them to each species for nothing buys you a lot of good will... though the Doctor doubted they even thought of that. Ponies might be easily frightened but unlike other species they don't lash out when afraid. They were so innocent and kind that it infected other species. Conquest through genuine compassion and a desire to... befriend every lifeform they met.

The Doctor might feel more at home on Earth but ponies had never once made him question why he was helping them.

“I sure love Jelly Babies.” The Doctor mumbled as he grabbed a hoof-full of the sweet candy and then dumped them into his mouth. “They’re so tart and irresistabl-ugh!”

He coughed a bit while patting his own back, making a mental note to never try to talk with his mouth full of candy. Ah what the hell, he’ll just ignore it as usual. He stood next to the TARDIS as he continued to chew his snack while staring at the Rift with a calm look on his face. After all, he needed some time to kill while he waited for…

*FLASH!*

“Speak of the devil…” The Doctor mumbled with a smirk as the white light died out, revealing seven figures.

One of them was a pegasus dressed in ancient combat armor. Another was a tannish pegasus dressed in what the Doctor would call “Egyptian” clothes. Next to her was a bearded Earth pony, nearly as tall as Celestia, who looked capable of crushing mountains with ease. Beside him was a lanky unicorn almost riddled with wrinkles. To her left was a blue Earth pony with a tall hairdo carrying a mask in her hooves. In front of them all were two important looking ponies. One was a unicorn dressed in magician robes, complete with pointy hat. He reminded the Doctor much of his "Merlin" regeneration. Next to him was a unicorn dressed in what the Doctor would call beggar’s clothes, not that’s a bad thing to begin with.

“Ladies and chums! Long time no see!” The Doctor happily greeted with a mouth full of Jelly Babies. He quickly swallowed the candy before speaking again. “Glad that you could all make it.”

He was suddenly met with a strong hoof around his neck as the bearded pony, Rockhoof, chuckled. “Aw lad! We wouldn’t miss it for the world! I hadn’t seen ye in a while! How’s ya kid and love?”

“Ach! Can’t breathe!” The Doctor choked before Rockhoof bashfully let him go. “Ah, they’re doing fine. How are you pals though?”

“We have been well, thank you for asking, Doctor.” The pony in beggar’s clothes, Stygian, responded with a kind smile. “We are glad that you have personally invited us to your TARDIS.”

One of the pegasi, Flash Magnus, stared at the TARDIS with a perplexed look on his face. “I don’t remember seeing your little blue friend being so…”

“Big?” The Doctor chuckled as he stared up at the TARDIS. No longer the size of an ordinary phone booth, the TARDIS was nearly the size of a skyscraper as it seemed to stretch on throughout the rift. In fact, the TARDIS itself was now occupying one of the rock-like islands floating throughout the Rift. He already got permission from the Yokai to park it here. “Yeah I think it grew a few inches. I just can't seem to find my ruler anywhere so I dunno how long it is now.”

“You’re gonna need more than a measly ruler.” The blue earth pony, Mage Meadowbrook, muttered as she gazed upon the TARDIS.

“You’re right. I need to find a meter stick but I think I lost that to.” The Doctor grumbled before he stood at the entrance of the TARDIS. Looking back at the 6 Pillars, and Stygian, the Doctor confessed, "I anchored her. It makes it so she is fixed to this spot until I release her, and let me tell you SHE WAS NOT HAPPY, but she came around after I explained I couldn't risk her taking the whole school with her next time she is in the mood for adventuring. I love the old girl but she is about as reliable as a fish finger, particularly the ones covered in Custard. Tasty but not very good for your health."

The Pillars just stared at his ramblings that was supposed to be an explanation, but it was Stygian that was able to piece something out, "School?"

The Doctor smiled brightly, “C’mon then! It’s better if we talk inside.”

The Doctor proceeded to open the entrance and stood by the side as he watched each of the Pillars, along with Stygian, walk inside the TARDIS. As The Doctor closed the door, he couldn’t help but chuckle at their amazed looks on their faces as they marvel at the spacious exterior of the TARDIS. After all, it was always bigger than it looked outside.

He turned around and blinked for a moment, noticing the ponies' faces did not look amazed. Instead, they looked freaked out. For a brief second, he wondered what made them look so horrified but as soon as he turned to where they were looking, his thoughts were put to ease.

Standing near the control console was a grayish unicorn with a red robe on his back. He looked up to give a respectful nod to the Doctor but paused upon seeing the Pillars stare at him with various looks of horror on their faces. Neither of them seemed to be pleasant. At that point, the gray unicorn coughed uncomfortably as he stared back at the brown pony.

The Doctor almost slapped himself in the face, feeling silly that he didn’t warn the Pillars and Stygian about…

“Sombra!” The Doctor cheered as he trotted to said pony. “Sorry for the wait. The Pillars and Stygian are here. Uh...”

He quickly turned to the ponies and back to Sombra with a sheepish and toothy grin on his face. “Want me to explain or you’re okay with telling them?”

“Tell us what?”

The Doctor let out a gentle sigh as he put on a serious look on his face. “Sombra’s...not like his past self.” He explained. “He went through some good ol’ friendship teachings and a good outlook on life thanks to, ugh, Celestia… and the Mane 6.”

"As I recall," Sombra eyed him, "It was you who convinced me to reformed."

"Oh I just laid the ground word," The Doctor waved off.

The tannish pony and wrinkled pony, Somnambula and Mistmane respectively, looked at each other before looking back at Sombra, who seemed uncomfortable with their uncertain stares. They saw him groan a bit as he walked towards them carefully.

“I understand the hostility you all have against me.” He said with a frown on his face. “What I have done is unforgivable and I am aware saying a simple sorry will not do.”

The Pillars stared at him without saying a single word, causing a silence that almost killed both Sombra and the Doctor. Finally, the brown pony jumped next to Sombra and placed a hoof on his shoulder.

“C’mon guys, it’s not like he’s going to do anything stupid like destroy the Tree of Harmony or brainwash all of Equestria to invade Canterlot or kidnap…”

“Doctor, please stop talking.” Sombra muttered with a massively uneasy expression on his face.

“Yeah… that’s a good idea.” Doctor responded with a red and sheepish face.

The magician, Star-Swirled the Bearded, let out a sigh before he let out a small smile. “Well, there is no denying the good work the Elements of Harmony and Cele-”

“Just the Elements of Harmony, Star-Swirled.” The Doctor bluntly interrupted. “Please don’t mention...her. Thanks.”

“Uh, noted.” Star-Swirled muttered before coughing a bit. “So it looks like we shall trust you for now.”

He looked back at the other Pillars and Stygian, all who shared uncertain frowns. Regardless, they shrugged and offered small smiles to Sombra, giving him some relief.

“Well now that is taken care of.” The Doctor muttered as he let out a stupid smile, obviously embarrassed at what just happened. “Sombra is here to help me out.”

“Help you with what?” Star-Swirled asked with a raised eyebrow.

“Imagine this.” The Doctor began as the Pillars begin to stand near the meeting table. “I’m thinking, no, PLANNING on making the TARDIS into a giant school.”

“A school?” Mistmane asked in curiosity.

“Yup. Help the lil’ ones know more about their odd manifestations of magic. Teach them how to control these Classes and such.” The Doctor continued as he walked around, glancing at the TARDIS interior. “Of course, who knows the Classes more than the Pillars, the humble Stygian, and my pal Sombra.”

Everypony else glanced at the silent Sombra before turning to The Doctor, giving them their undivided attention as he continued on.

“If I recall, each and every one of you has a class of your own. Well except for you Stygian, but we like you anyway." The Doctor still had trouble understanding when he was being rude, "Magic does come out in all sorts of interesting ways, doesn't it? You all have tried your hands, errr hooves (still can't get that right), at teaching these confused children yourselves. It is hard to be imbued with such power and not have the slightest clue where it comes from. They are often shunned and misunderstood. Ponies misunderstanding of Sombra's shadow bending is what turned him to a life of evil."

The ponies looked back at Sombra, who was conveniently looking somewhere else.

The Doctor went on, "We need to save these children from such a fate. You are told you're a monster long enough and you start believing it, right Sombra?"

Sombra just groaned in exacerbation.

"My school will not only help these kids learn control, but it will also show them they are not alone well raising awareness in the public," The Doctor explained, oddly serious for a moment, "That way none will ever again go through what we did. Then, if the children so desire, they can put their gifts to use defending all those born without their gifts. Or they can live a simple life as civilians, helping in their own just as special ways.

"I realize you had a school of your own, along time ago, and though short lived I see how much good it did for your world. I believe, with my resources and confidence, this school will thrive for countless generations. We will show the Galaxy itself Classes are not something to be feared."

The Doctor looked around, seeing their determined faces, “I wish to hire you all. Starswirl here will be the Deputy Headmaster and Stygian will be the Head Counselor. The rest of you will all be the first teachers when this place opens up.”

The Pillars began to whisper to each other upon hearing this before The Doctor changed his tone. “I understand this will be some darn hard work, and it’s going to take a lot of years just to get approval from the Senate for an interplanetary school and set everything up. Believe me, I hate doing things the long way, but for this? This will be worth it. I know we can do this. All I need are your approvals. That and students.”