Comes the Sunset - How It Would Have Ended
The army of Imperial Grevyia - or at least those parts of it which aren't involved in mutiny on the streets of Canterlot - marches out with drums and trumpets, accompanied by great fanfare, to crush Rarity and her gathering forces. The worsening weather turns against them, and most of the griffon mercenaries desert, but the zebra forces struggled on through the sleet and snow, even as the cold takes its toll on their war elephants. Matters are not helped at all when Bon Bon, using her secret agent training, sets fire to the Grevyian stores, leaving them stuck in the middle of a worsening winter with no food. Virtue responds by cutting loose all the pony levies, since they are unreliable and a drain on resources, while trying to chivvy his troops along with the promise of plunder and food once they capture Rarity's camp. Nevertheless they begin to suffer desertion.
Applejack, Pinkie Pie and Maud are released by Sunset, and start off by shadowing the zebra army, then by outpacing it once its many difficulties become apparent. They bring word to Rarity of the approach of the enemy forces, and Rarity - now reinforced by Cadance, Shining Armour and the Crystal Knights - decides to advance to meet them, offering battle away from the town to spare the civilians in case the zebras emerge victorious.
Derpy and Aeternitas travel through the war-torn countryside, which is becoming filled with desperate refugees, and the equally desperate but more vicious bands of bandits and deserters who prey on them. Aeternitas is incredibly cynical about all of this, but Derpy takes it upon himself to act as his conscience, and gradually draws a touch of compassion out of the old alicorn. She finds out the reason why he abandoned his daughters: it was easier than staying to watch the tragedies he knew where in their future befall them, the madness of Luna and the long, lonely millenium of Celestia's rule. That's why he acts like such a rampant dickhead, it is easier to keep people at a distance than to let them in and lose them. His cynicism is challenged by Derpy, and her optimistic view of people is proven right as she gathers both refugees and brigands to her, uniting them in some semblance of harmony for their own survival. Aeternitas is insistent about reaching Rarity's host before the zebras do, but Derpy is equally insistent about staying to help those in need. Aeternitas begins, against his better judgement, to grow attached to her.
Winter descends on Canterlot swifter than any enemy army, and most of the fighting in the streets grinds to a halt as the snow and the icy cold winds make it perilous to so much as go outside. Fighting is restricted to small skirmishes between Sunset's loyalists and the rebels and their pony allies. Sunset descends deeper into madness, becoming more and more reclusive; when she does see anyone, she soon frightens them off. Only Celestia can gain access to her.
On the edge of the Whitetail Wood, Fluttershy's group runs into Razor, Candy and the Cutie Mark Crusaders, who have the Box in their possession. They are attacked by the indefatigable Emerald Ray. Glory Seeker steps up to fight him warrior to warrior...and gets her flank handed to her with all the trimmings. It is only the arrival of a group of deer from inside the wood that drives the crystal pony off, for now.
Fluttershy makes her appeal to help to the leaders of the deerish, but soon finds the complicated politics of the wood in her way. Whitetail wood is occupied by the deer, the wolves, and the werewolves, descendants of ponies cursed by Luna during her descent into Nightmare. The wolves hate the werewolves, and if the deer abandon the forest in force, they will attack and great harm will be done. The werewolves cannot leave the wood because they aren't safe to be around normal ponies (as a result of this, none of them have cutie marks, since they can never go and find their special talents). The wolves will not make peace with the werewolves because they view them as fundamentally unnatural abominations. Fluttershy's diplomatic skills are put to the test (as is her compassion around some pretty frightening creatures, prone to exploding into rage at any moment), but through patience, kindness, and a dogged refusal to give up she is able to win the respect of both the deer and the wolves, as well as becoming the only pony able to exercise any control over the werewolves. The deer and the wolves both agree to join her host, as does a young werewolf named Silver Blaze who is desperate to see the world beyond the forest.
Inside the Box, Twilight, Dawn, Trixie and Chrysalis continue their way down the golden road. In the Party Palace of Laughter, they are tempted by a desire to stay in an endless revel, with cakes and dancing and music and ice cream and punch that never runs out, but they resist and insist upon leaving. Laughter becomes briefly terrifying and tries to frighten them into staying, before Twilight reminds her that a pony who really cared about the joy of others would never try to keep anypony somewhere against her will.
Next, they encounter Generosity again, this time accompanied by a forlorn looking mare named Forsaken (Derpy), who was once queen of this land, but has now been rejected by everyone for reasons that are not her fault. To prove themselves generous, the four must give up the gifts that Generosity gave them at the start of their quest. Of all of them, Trixie is the most reluctant, but eventually they all do it, and recover the last of their memories.
Now that they remember everything, Twilight and Dawn start to fight, to the great amusement of Chrysalis. They come very close to brawling right off the road until Trixie reminds them that they have more important things to worry about, like stopping Sunset. That night, or what passes for it, Twilight and Dawn achieve a tentative reconciliation, with Dawn admitting that she was wrong to do what she did, and conceding that Twilight is, indeed, the better mare and the better friend by a long way, and that Celestia made the right choice. Twilight, for her part, says that she can understand why Dawn was desperate to get back into Celestia's heart, as Celestia is the kind of pony that draws others to her. That does not, Twilight makes clear, forgive what Dawn did to try and get back into the princess' good graces.
While that is going on, Emerald Ray is back, and he's kicking eight kinds of flank amongst Fluttershy's group. No one can withstand him, until Candy whispers the incantation to open the box one last time together with the words "Dawny, come save us."
The box opens, and Emerald is no match for Twilight and Dawn, who finally get rid of him. They reunite with their friends, and learn that an army is marching against Rarity. Twilight leaves the decision up to Fluttersy, who decides that they will go and help Rarity with what they've got, rather than worry about the griffons. Chrysalis refuses to help, and departs to rejoin her people.
Derpy, Aeternitas and all those they have gathered to them (including Bon Bon and the ponyville conscripts) join Rarity's gathering army the day before the zebras get there.
Battle is joined between Rarity and her ponies on the one hand and Virtue leading the zebra army on the other. Rarity has chosen the ground, and fortified it, and from their defensive position the ponies repel several textbook frontal assaults from the zebras. The vanguard of Fluttershy's forces begin to arrive on the field, but Virtue has the word put about that it is Sunset Shimmer with the remainder of their strength come to reinforce them, lest his troops lose heart.
Without many options left before Fluttershy's allies arrive and overrun his flank, Virtue sends in the Grevyian Imperial Guard to break Rarity's line. They very nearly do it, but Shining Armour leads his crystal knights into a well-time counterattack just as Fluttershy's dragon arrives on the battlefield. The cry goes up 'Treachery! We are betrayed!', and the zebras begin to break and flee the field. Rainbow Dash duels Lightning Dust and defeats her handily with the help of Fluttershy, thus proving the superiority of friendship over pride and arrogance.
Derpy is killed in the fighting, and Aeternitas muses that, before he met her, he would have convinced the loss of an unimportant pony like her a small price to pay. But she has shown him that she is the most important mare in the universe, if only to her two daughters (echoing her words to him about the importance of her daughters to her), and so he uses his power to bend time to save her life, at some cost to his own life force.
The shard of Moloch contained in Virtue takes possession of him and starts whaling out, putting Shining Armour and Cadance up against it until Glory arrives. She fights the possessed Virtue amidst flashbacks of their childhood together, begging her old friend to reassert control and give up. She almost dies, but Virtue cannot brings himself to harm her and overcomes the possession. He surrenders, and is put in chains. Lots and lots of chains.
The Mane Six reunited amidst much jubilation. Rarity offers to let Twilight take charge but Twilight refuses, since Rarity was appointed by Celestia and has done a fine job since then. There is some debate over whether the windigoes are not more dangerous than Sunset, but Aeternitas tells them that the only way to stop the windigoes is to stop Sunset and Moloch and restore harmony to Equestria.
The combined army marches on Canterlot, picking up zebra stragglers as they go.
which is defended by a shield stopping anyone from getting in. The heroes are joined by none other than Chrysalis, leading a changeling army while grumpily trying to ignore the signs of developing conscience. While the changelings cause a distraction by hammering their bodies into the defensive shield, Twilight and Dawn are able to open up a small gap in the shield elsewhere. A picked group (Twilight, Twilight's friends, Dawn, Dawn's friends and Trixie) sneaks into Canterlot. Dawn's group works on getting the shield down, while Twilight's group tries to free Celestia and Luna.
Each group gets embroiled with a shard of Moloch: Twilight's gang battles the Shrike!Moloch, and Dawn's the Precious!Moloch. However, Aeternitas has given them a means to weaken the demon's hosts, and both are defeated. Shining Armour leads the army into Canterlot. In their camp, Virtue breaks free of his chains...
Trixie goes straight to the throne room and confronts Sunset. Or rather, the Great and Powerful Trixie returns to Canterlot for one final stupendous performance! Trixie, who has been given a magical power boost by the box, is able to dodge Sunset's attacks, all the while pleading with her to just give up already. Sunset is too far gone to realise what she's doing.
Twilight and Dawn and all their friends burst into the throne room, but it is too late: Moloch arrives. Everypony fights desperately to stop him from fully emerging into their realm, but as his energies begin to consume Canterlot it looks hopeless. Sunset, having a moment of lucidity, tries to physically push him back into the dark dimension he is trying to crawl out of, using all her magical power to do so. It works, and Moloch falls, but grabs hold of Sunset as he does so: if he cannot conquer Equestria, he will drag her into darkness with him.
Dawn grabs Sunset and refuses to let go, refusing all of Sunset's entreaties to just let her fall, since everyone deserves a second chance. All Dawn's friends grab on and start pulling, but even together they are no match for the force that Moloch can bring to bear. Trixie and Twilight try to help out, but it is still not enough.
Virtue charges into the throne room, leaps through the portal and lands right on Moloch's face, hitting him with everything he's got. Sunset is released, and Dawn et all pull her back into Equestria as the portal closes, trapping Virtue in the dark dimension with Moloch. Glory weeps, but takes comfort in the fact that he finally, finally did something unambiguously good.
Celestia and Luna reconcile with their father, but the strain of saving Derpy and giving the girls the means to weaken Moloch has taken a lot out of him. Aeternitas disappears, it is ambiguous as to whether he is dead or just vanished. Twilight unlocks Glory's people from the captivity in which Sunset had placed them.
The big question is what to do about Sunset. Dawn begs for Sunset to be given over into her charge: she intends to go to Grevyia, to help sort out the turmoil consuming that country, which is fair enough since it is partly her fault that things have gotten this bad over there. And since Sunset is also responsible it's only right that she should have to muck in as well. Celestia agrees, on condition that Dawn keep her under control. Dawn's friends agree to go with her to Grevyia, and they set off, to see what second chances can turn into.