Time Skip:
Just glossing over some key events, that wouldn't be fun for me to write.
The War Intensifies :
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.
Tempest :
During the World War, Chrysalis finds Tempest and offers her assistance. Chrysalis tells her she has the knowledge to fix the Mare's horn, but currently lacks the power to do it. She needs the power of the Alicorns, using a staff made from the root of the tree of Harmony, and Twilight as the focus, since she is the Element of magic. She promises to fix her horn in exchange for the staff, once it is completed.
Chrysalis says that she knows Tempest has seen the tree of Harmony in her travels and can harvest the root with her raw magical power, thanks to her broken horn. Tempest agrees.
Chrysalis sends an unnamed changeling, who literally has no name, with Tempest to keep an eye on her. Tempest comes to call the Changeling "Grubber" after hearing Chrysalis refer to it as "Grub". Tempest and Grubber go to the tree of Harmony and she uses her broken horn to launch enough destructive force at the tree to slice off one of it's roots. The tree attacks her back and they are able to just barely escape. Grubber becoming badly injured to protect her. This endears him to her a bit yet she still treats him relatively poorly as she believes he will eventually betray her.
Tempest then leads an attack of changelings against Canterlot and uses orbs to trap the other four principles as stone statues, including Flurry Heart. However Twilight is able to get away with her friends. Tempest tracks the 6 to a Yokai Cat named Capper who offers to sell the ponies to her, but he has a last minute change of heart and let's them escape, while tricking her to follow him. She takes him prisoner and well interrogating him onboard her Airship, Grubber spots a Sonic Rain-boom.
They find a group of Yokai bird pirates, who once again let the mane 6 escape. Becoming frustrated Tempest destroys their ship with the crew and Capper trapped on it, leaving them to die as they fall from the sky... and forgetting The Yokai birds, can shapeshift into birds that can fly. As they take Capper with them.
Tempest finally captures Twilight, when she becomes isolated, after trying to steal an artifact from their allies the Sea ponies. Tempest gloats over Twilight losing her friends, as Tempest believes friends will always turn their backs on you when things get hard.
Chrysalis absorbs the other Alicorns magic, using Twilight as the focus. After the changeling Queen has the staff she tries to use it to kill Tempest. Grubber jumps in the way of the blast, sacrificing his life for her. This shocks Tempest to her core, as she can't imagine anyone actually doing that for someone else, outside of a story book.
Tempest and Twilight fight Chrysalis, the rest of the Mane 6 appear with the friends they have made over the course of the Adventure. The seapony princess has the orb Twilight tried to steal and uses it to transform the Mane 6 into their Rainbow forms. They overwhelm Chrysalis and are able to get the staff away from her. She teleports away and her army occupying Canterlot immediately do the same.
While the ponies celebrate, Tempest mourns over the loss of Grubber, who she just now realizes was a true friend.
Discord appears to her at the end, and promises to look after Grubbers soul for her, but it is the most he can do.
Sombra :
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 warring species call a truce to save their world from the Wendigos.