Notes:
These are ideas I had for this story, but don't have the time to fully write out. So here is where the story WOULD have gone.
Chapter 3:
The war intensifies.
Chapter 4:
Queen Nova sat on her throne, as she observed the surfacer, but he wasn't like other surfacers. He came from far away, the other side of the planet. He was a shapeshifter. His army stumbled on them some months ago, traveling the oceans of sea serpents to find their enemies nest... Nova understood a thing or to about trying to proactively protect your citizens.
He called himself "Thorax" leader of the "Fae Beetles", what everyone was coming to call his breed of "reformed changelings".
Nova sighed, "My people have been warring with the Hippogriffs for generations, although we once lived peacefully in the same kingdom. I guess you could say I 'get it'. This war has cost us much."
The changeling, in the shape of a sea pony (perhaps to make her more comfortable?), looked at her with such sympathy in his eyes, "We are hoping to end our own war soon. With the death of our former tyrant we will be able to turn to diplomacy, to convince the other rulers to lay down arms."
"What do you need from us?" Nova asked, "We may control the seas, but we are kinda useless on the surface."
"All we want is medicine and nutrition," Thorax insisted. "All my resources are devoted to the war effort. We need better potions and food to feed our allies. You help us and I promise, my forces will help you. We will protect you from the Hippogriffs."
And that is how the Hippogriffs got involved in the global war.
Chapter 5:
Summary:
based on the Season 9 premiere "The Beginning of the End" only without Twilight preparing to take over Equestria.
Something is wrong with the tree of Harmony. As the war rages, it gets weaker, until one day Sombra appears to finish the job. He destroys the tree of Harmony, releasing the entire Wendigo species that was contained inside.
Sombra proceeds to brainwash the population of Ponyville, into a fit of depression and rage so that their conflict feeds his masters. The Mane 6 battle him, but he defeats them. Then the Wendigos spread all across the planet. The chapter ends with the warring species calling a truce to save their planet from the Wendigos.
Chapter 6:
Doctor Whooves goes to Sombra, and convinces him to come with him. To abandon the Wendigos' plan, and to live as his own pony.
Chapter 7:
"So..." Chrysalis huffed as she watched the armies celebrate. She stood in a tent with the other global leaders... discussing peace. Her fear of the Wendigos return was the only reason she was considering it. Her plan had almost worked. She had turned against her 'allies' ready to conquer all the world... when the Wendigos appeared and ruined everything.
She long since thought the spirits of conflict were extinct... the now three way war was forced to end as they all united against the Wendigos. They won in the end, driving the beast back... but at what cost?
"That's it, is it? The battle is won and we forget we've been slaughtering each other for over a year,"
Thorax sighed, "I don't think the world will ever forget."
Chrysalis scoffed, "Naive grub."
Celestia walked over to her, standing by her side and watching the celebration, "Forgiving, is not the same thing as forgetting."
"Changelings once lived like this," Chrysalis looked around at her children, all her children, laughing and drinking with the other races. "We embraced you... and thought you returned our feelings. We protected you and helped you... and in return you enslaved and butchered us... crushed thousands of innocent eggs... I won't make that mistake again,"
Chrysalis began walking off but stopped, looking back at Thorax. "I will admit. In my need to protect you, from my mistakes, I forgot what I was trying to preserve. I now realize I can't force you to see things my way... and perhaps I should change how I do things a bit, but never forget... everything I did... was out of love for my children... for you...
"but I will finally accept you are destined to repeat the worst of my decisions... I'll be here when it all blows up in your face. See you in a few thousand years."
Chapter 8:
After their defeat, The Wendigos are approached by a race of "Sub-ponies" called "Time Ponies". They claim to bring a gift from Sombra. Before offering the Wendigos many berries, which come in flavors of: despair, hate, anger, violence, and fear. Which meet all the nutritional needs of the emotional parasites.
The bushes even grow in winter. So the Wendigos can farm them in the snowy wasteland of their territory.
The Wendigos may have lost their war, but because of Sombra (who convinced the Doctor to help), they gained the ability to become truly independent, without need of hurting any Sapient creature.