Opening theme is down below here.

Back in the days of yore, a unicorn wizard named Star Swirl and his group: the Pillars of Equestria, served to protect the land of Equestria. But when the one who brought them together was believed to be covetous of the Pillars' power, they cast him out. The pony thus turned to darkness for power and revenge, and transformed into the Pony of Shadows. In order to stop the beast, the Pillars had to sacrifice themselves to save Equestria. But Naturus had other plans when he arrived there.

Naturus tried to kill both them and the Pony of Shadows, but the Pillars didn't want death, so Star Swirl cast a spell that imprisoned Naturus in the form of a-

"Yeah, yeah, narrarator, let me take it from here.

"Yeah, that know-it-all guy turned me into a seed and planted me to protect his stupid land. I was not immune to magic at the time, and then, I developed that immunity. So yeah, whiny-boy and his P-team were sent to Limbo with that ugly ball of darkness, leaving me there to rot."

Yeah. How-

"Yeah, unlike most, I was awake for my entire imprisonment. Watching them control the weather, raise the sun and moon, and even bully animals into submission. Not pretty. Luckily for me, as you saw earlier, I escaped from my prison and supposedly killed the alicorn sisters. Don't you worry yourselves, they'll be back... I'll let them see the new world that is here now. I'll let them live."

Okay, Naturus. Why are you even here?

"Oh, I just stopped here to say hi."

What about Star Swirl, Naturus?

"Oh, him. That reminds me, I'll take the Pillars to my castle as soon as they return from their gloomy imprisonment. I've been thinking about-"

Get out of here. And go to near where they return.

"Gah, you are such a spoil-sport. Nevermind, I'll leave."

Now how did he get here? No matter, as I was saying, the P-team will return right about... NOW.

It was almost midnight.

On a mountain, there was a Stonehenge-like rock formation. Naturus and his forces were camped outside, waiting. And suddenly, a bolt of lightning struck the center. Six ponies in different attire lay unconscious. A seventh pony, an alicorn of darkness was the only one awake in this whole time.

"Unconscious, eh. That will leave me just enough time to engulf the world in darkness!" the shadow alicorn said before he heard the bushes rustle.

"Well, well, well. So we met again, old chum."

The shadow pony heard the voice. That voice. It belonged to the guy who tried to kill him.

"Naturus..." the shadow pony said as the being burst forth. Naturus, in his glory and in a bunch of robes. He was there like he was never turned into a seed in the first place.

"In the flesh... wait, do I have flesh? Do you have flesh for that matter?" Naturus said jokingly.

"You my have turned back to your true form, but you are not going to beat me in my game..." the Pony of Shadows said as he attempted to blast Naturus, but to his surprise, the blast bounced off.

"Gah, how?" he said in shock.

"My body may have been still, but I still had a few tricks up my sleeve. During my imprisonment, I have developed an immunity to magic. Now, it's my turn to attack." Naturus said as he went in front of the moon and used its energy to kill the shadow pony for good.

"So apparently Moongeist Beam would be really effective on forces of darkness. I better tell that to my old friend Lunala about this." Naturus replied jokingly with his reference to those 'Pokémon' games he had heard about, but never played. He never met a version of Lunala to be honest, neither did he meet a version of Solgaleo.

Oh how millions of years fly by for a deity like him. His creators were long since dead, and he now rules a magical pony land of happiness and friendship. Wonder how his REAL old friend Peepers is doing at his home in Koosland. He was the one who actually existed in this universe.

He knew Peepers like his own brother, if he had one to begin with. He flashed back to when Peepers told him his story.

It all started when the girl was a dumb little baby. Her mind was completely blank But then, she had an idea, and that idea was Peepers himself. And since the girl had may other things to think about, Peepers was left in charge of that same girl's imagination. He gave so much happiness for the Koosfolk to have, that he was rendered a grump for a time.

That is until this Hookocho character showed up and almost destroyed Koosland when trying to reverse Peepers's power to increase his own. Peepers mutated into a huge dragon and crushed Hookocho with one foot, regaining some of his lost happiness in the process.

Naturus flashed a bit forward to when the girl died, he never saw Peepers again after that moment on. Did he live onward or did he die with the girl? And what of Koosland? Did it die to? All he knew what that Koosland was in a galaxy most likely billions of light years away with no knowing what happened to the island. Without the girl as a catalyst for a portal, he does not have any way of contacting Koosland. Even his powers had limits of their own.

He wondered if they even remembered him or he remembered them. All he knows is that ever since he lost contact, he was growing bitter and agitated knowing that he can no longer see Peepers.

"Master... Master..." one of the guards said as Naturus snapped back to reality.

"Alright, take the Pillars to the dungeon. And make sure they do not see them, especially Cadence. I do not want her memory to be triggered just yet." Naturus said, pointing to the six ponies.

"Yes, milord." a random guard said as they put them in a metal box.

The guards put the box onto a large metal cart pulled by two Anatosaurs along with some crates of food and supplies.

As for Naturus himself, he simply teleported back to Natropolis in a flash of light.

This is going to be a LOONG day.

Author's Note

I put Dexter's Lab in the timeline because I wanted to see who could have the potential besides the U.S. Government to be able to create Naturus. The purpose of Naturus was to guard and protect Earth. Who created him, it is unknown.

Naturus came to know Peepers when discovering a portal. They told each other their origin stories and all that. After the death of Dee Dee, it is unknown what happened to poor old Peepers, but that has made Naturus angry and lonely. In fact, Naturus created the ponies to remind himself of the land of Koos before he got consumed by his own anger.

This version of Naturus does not attack without a reason, so if he takes the path he does in TRoLN, Starswirl would be one of his major targets since he turned Naturus into a seed.

Which TV shows should I add to the timeline, I don't know. But right now, it goes something like this:
Dexter's Laboratory -> Creation of Naturus (Earliest possible point) -> Big Bang Theory -> Creation of Naturus (Latest possible point) -> Transformers -> Star Trek -> Nuclear War -> Adventure Time -> Star Wars -> MLP (All Generations in unknown order)