UNDER REVISION, Sorry about the mess!

Canterlot City, 1 day later...

An ashen colored unicorn stallion sprinted towards the audience chamber within Canterlot Castle, many tomes and scrolls flying just behind him at an unearthly pace. Gasping for breath, he finally reached the chamber and burst through, temporarily tripping on his robes bearing the Scholar's Sigil.

"Y-your Highnesses!" The stallion wheezed, recovering from the fall and bowing halfheartedly.

"What troubles you, my little pony?" Celestia spoke, worry strewn about her muzzle. Luna paused in her stride to her bedchambers for her rest and relief of nightly duties, a hint of concern crossing her features as well.

The stallion caught his breath before continuing. "I-it's the anomaly; It opened a portal!" He all but shouted. Now the two rulers had his undivided attention. Luna whispered to her assistant on the side, asking her to bring a quill and some parchment. She had a feeling this anomaly would warrant immediate response.

"Has anything entered our realm?" Luna inquired as soon as her assistant left, only to receive a relieving "no" from the Scholar. "Good. Report your findings to your superior, both my and mine sister's personal guards will be posted near the Anomaly. We will also send routine patrols of all other guards to be stationed around its perimeter."

"Thank you, for bringing us this information." Celestia said, revealing a small smile for the young Scholar. "You've earned some rest, my little pony. Feel free to use the guest bedchambers to relax and calm your stirring mind. Our staff will guide you on the way out, as well as bring anything you request. Thank you for your due diligence in bringing us this message."

With a small but grateful "thank you", the stallion left the audience chamber followed by Celestia and Luna's personal maidens. The Princesses' smiles disappeared as soon as the door shut.

"Do you think it is one of the Riders, sister? Given the coincidence of us losing the Elements..." Luna asked, her tone worried.

Celestia sighed. "I don't know, Lulu. If it is one of the Riders Four as foretold by our dear friend Clover, then we are all doomed."

"But what of the contingency plans? Do we not have those still hidden within our archives?" Luna asked, only to have Celestia shake her head.

"Most were designed for yo-" she paused, still guilty from what happened all those years ago. "*ahem* Nightmare Moon's return and were burned long ago, save for one- The only one proven to be effective." She sighed solemnly. "It seems the Fates have planned for this to happen no matter what. The revival of the Tree of Harmony is far too convenient to think otherwise..."

Just then, Luna's assistant returned, giving the midnight blue Alicorn the requested quill and paper. "If it be truly as dire as we suspect sister," she began, hovering the quill and parchment, and hastily scribbling away a letter addressed to Shining Armor of the Crystal Empire. ", then we must gather our forces and prepare."

Nodding in agreement, Celestia ordered the guardsponies stationed within the room to attention. "A threat to our country, nay life as we know it, may be arriving if it hasn't already. Spread the word amongst our troops;" the monarch sighed, dreading the consequences her next words might bring. "We must prepare for Ragnarök..."

Meanwhile in the Castle of Friendship, Twilight emerges from her slumber and immediately jumps right back into her research. Knowing better than to convince her to come eat breakfast, Spike made a small bowl of cereal and placed it in the Library on the desk she was reading at. She will not finish her research however, because the next passage will terrify her like none other...

It began like it always did: A date and point of reference was scrawled in the top corner of the first page the passage started in. However, instead of a numerical reference, this one was dated like a journal:

Year 245, Harmony's Solstice

As the days go by, it seems the visions guiding me to these forgotten ruins riddled with ancient Alicornish lore are slowly becoming more vivid. Now I can recall seeing these ruins as if I knew them my entire life. Before the Princesses reigned, I asked my Queen what these visions entailed, only to be judged as if I were no more a miniscule dust particle. Though she had changed after the two Alicorn Sisters revealed themselves, I had yet to find an answer to this gift I was given. Then one day, one of them visited: the younger one, Selene de luna pacificae, approached me hearing of my gift from Queen Platinum herself. Luna, as she liked to call herself, spoke. "Doth not feareth thy gift, f'r me and mine own kin possesseth t too" she spoke in that archaic language the nobles invented, eliciting a rolling of my own eyes.

"Speak plainly" I uttered. The shock on our new Princess' face was priceless.

"What is thy nameth, peasant?!" She looked serious, but I knew the truth. She tired of it just like I did. I could see it in her eyes.

"Clov'r, but thee can calleth me misseth peasant if 't be true t pleases h'r majesty" I bowed mockingly. Her mask began to break if the snicker was any indication! My cocky grin must've shattered it the rest of the way, for it brought forth a wave of laughter like no other.

A few moments passed before we both settled down. "You have brought much joy to us this day, dear Clover!" She dropped the "language" much to my enjoyment. "We can tell if us and our Sister are to succeed with thyne new world, we simply must have one clever as yourself among our most trusted of friends. And thus, I was called Clover the Clever, one of the Three to unify Equestria...

The journal entry shocked and bewildered Twilight at the same time. "I hold a journal fragment... Of Clover the Clever?! Ohmygosh this is the best, squee!" Her inner nerd came out and began to prance around like a schoolfilly at recess. "This is huge! Nopony has been able to find any traces of her aside from mere mention in folklore and historical accounts!" That sentence gave her pause. "This author, this 'Vigil' character: They have knowledge they shouldn't." She shook her head. "Nah, that's crazy talk! Just because you haven't read it, doesn't mean it's some sort of forbidden knowledge!" The Princess chuckled a bit, continuing further:

Year 300, Luna's Fall

Nearly a century has passed and our two Rulers have fought a great battle with the lord of Chaos, Discord himself. He was the last of his kind, and his imprisonment I knew in my heart was just, but as I feared, it only gave truth to my recent visions. In my old age, I have noticed things lurking from the shadows, conspiring to topple the great nation that I and my friends now long gone, have strived to protect. Only ever known as the Shadow, this dark presence is always at the forefront of my mind, ever since my first vision surrounding it.

I tried telling someone, but as with any old mare, my old ramblings are pushed aside and branded as ramblings from an old prophet. The only one to listen was Celestia, and I fear she didn't take it to heart as well as she should have.

"In the vision, I see two sisters fighting.
One was surrounded by Harmonious light, the other bathed in darkness, possessed by the Shadow." I explained to her. I waited for a reaction, only to receive a nod of the head to continue. "The sister in the light was remorseful. There was a burden placed upon her that no sister should bear."

"These sisters, are they of me and mine own sister? Could you make them out?" Celestia was terrified at the implications this could mean. Looking back to that discussion, I cannot blame her for my next vision. Fate is fickle that way it seems...

"No, your highness," I spoke. "The figures were shrouded. The message was clear, however: a choice is given and what choice you take is going to impact the nation for thousands of years."

She didn't believe me...

"Fate isn't always black and white, dear Clover" she talked down to me, as if I was no more than just another senile old crow squawking in her ear. Her decision that night gave me a very last vision, before the irony of Destiny caught up with me and robbed me of my sight. Even as my assistant records these words, I can see her shake and hold back tears, both from my inevitable death likely to come in the following weeks, and the vague prophecy I gave her to pen...

the page was stained with ancient tear spots long since dried up. What she read next made Twilight's heart grind to a halt:

To the one reading this, you need to know that the Final Prophecy I give you will shake the very foundations of everything you hold dear. Find loved ones if you must, and pray this is just the senility of a dying mare:

When Harmony is returned and Chaos tamed, He will come, as he comes to all of us in the end. The Pale Rider will save the souls of Man, yet doom Equestria; the sacrifice to atone for his brother's sin paid in full. Look for the signs- a doorway of unknown origin, twin scythes severing the head of the horse, and the final sign:
the roar of His dreaded companion, draining the souls of the wicked with its piercing gaze...

Death approaches, young ruler. Run while you still can...

Twilight dropped the book in utter terror, sprinting towards Canterlot in fear of the safety of the Scholars observing the anomaly.

Death is coming...

Author's Note

For those history buffs reading this, the interpretation of Ragnarök for this story is the translation that refers to the "Twilight of the Gods", and not the other one referring to the "Fate of the Gods".

Why? Because this crossover involves ponies darn it!

Lore building time!(not necessary for plot relevance, only there for flavor) So, Alicorns were near extinct when Celestia and Luna were first approached to be leaders of the new Equestria, making their language a dead language, even way back then. Celestia could read it, and Luna could speak it, but that was as far as the knowledge of their culture goes. New ones not born naturally would obviously lack knowledge of their culture, especially if their species is near extinct.

The first sign of Pony Apocalypse has been revealed so far, what of the others? Some good foreshadowing about potential locations, so keep that in mind! As always, any questions, comments, concerns, just send them my way! Ill answer as best as I can!