We start in an alternate universe called The Shimmerverse. In this universe, Nightmare Moon started several dark cults and inspired several dark sorcerers before she was banished to the moon a thousand years ago, and these villains threatened Equestria through the ages. Princess Celestia's student Sunset Shimmer remained loyal to her and she was eventually officially adopted by Celestia. Sunset hatched a dragon egg and was the one who was sent to Ponyville to make friends. When Nightmare Moon returned, Sunset and her friends fended off her army and assembled the Elements of Harmony to transform her back into Princess Luna. However, Luna still hated her older sister, so Celestia kept her confined in the Canterlot castle while trying to get through to her.
One morning, Sunset is feeling restless and hikes into the Everfree Forest. She finds a dagger laced with dark magic and with a lunar symbol. Her fears are confirmed; some of Nightmare Moon's army escaped and are hiding in the forest. She knows the smart thing would be to leave and report this to her mother, but she stubbornly wants to get absolute proof and ventures deeper into the forest. She follows tracks and is shocked to see an entire reserve army, consisting of several dark magic-mutated ponies and monsters like dire wolves and hulking, reptilian behemoths.
They are being commanded by some figure packing a lot of dark magic surpassed only by Nightmare Moon herself. The army goes on ahead while a warlock and some wraiths remain behind. Curious, Sunset decides to see what this smaller group is up to. She is briefly surprised when the group uses a cloaking spell that renders them invisible unless one gets within a certain distance, and realizes this must be why the army had not been noticed by Pegasi flying overhead as they might have been using similar spells to cloak their camps. The warlock, a Unicorn heavily mutated by darkness, goes to an obsidian pedestal with a glowing blue sphere on top and orders the wraiths to cover her while she summons reinforcements.
The warlock pours energy into the sphere and it starts mass producing Shadow warriors, masses of solid shadow. She also notices these Shadows are an odd color tint she's never seen before. Moreover, each time the spell is cast the resulting number of Shadow warriors pulled out doubles and is growing exponentially. Horrified, Sunset declares she must stop this before Equestria is overrun and attacks as soon as she has an opening. She blasts the Wraiths with her flame spells and then attacks the pedestal and the warlock. The two have a magical duel, but the pedestal reacts to their conflicting energy and creates a portal. The pedestal explodes from an overload, knocking the two combatants senseless. Sunset regains her vision and hearing to find the pedestal gone and a large winged creature covered with an inky substance coming out of the portal. The warlock is mortally wounded from the explosion, but she laughs and proclaims Nightmare Moon shall return before her body crumbles to ash.
The creature approaches Sunset. Thinking it was a Shadow beast summoned by the warlock, Sunset launches a flame attack at it, but is shocked when it barely has any effect. Her flames have usually been able to kill creatures of darkness in a few shots. Instead, the flames burn off the inky substance to reveal a featherless Gryphon, Rodan of the Terran Defenders. Rodan has no idea what is going on or why this Unicorn attacked him, and he tries to talk to her, but she unleashes a flamethrower spell. Annoyed, he counters with his Uranium Ray, using only a small percentage of strength to avoid killing her. The ray pierces her flamethrower and nails Sunset, knocking her into the bushes. Rodan remembers what Godzilla Junior did when he crashed into Canterlot and realizes this fight could be all a big misunderstanding that he's going to try and not escalate just in case. He calls out to her and says if she stops attacking him, he'll fly her to the nearest hospital if he hurt her any.
Sunset roars at him, loses her temper, and attacks with flames hot enough to destroy boulders. The battle turns into a stalemate. Sunset has the ability to absorb fire and heat to bolster her magic, but Rodan has a similar ability. Though their blasts can cause each other pain and knock each other around, all they are doing is powering each other up. Rodan realizes this is going nowhere and calls for a timeout. This baffles Sunset Shimmer, as all of Nightmare Moon's creatures are fanatically devoted to her and would never stop fighting. He asks if he is still in Equestria and she confirms this. She asks if he is a member of the Nightmare Army and he has no idea what that is.
She explains that the Nightmare Army summoned him from a portal and they are in the Everfree Forest. Rodan is extremely annoyed at the thought he's been sporadically warped to another place like last time, only taking comfort in the knowledge he seems to still be in the same realm he was a few minutes ago. The last thing he remembers was taking a nap with Rainbow Dash in the clouds, so he has no idea how he got here. He asks which direction is Canterlot so that he can talk to Princess Celestia to sort this out. Sunset demands to know what business he has with her mother. At his confused reaction, she introduces herself as Princess Sunset Shimmer, daughter of Princess Celestia. He laughs and starts treating her like a little kid playing pretend. He says he paid attention and the princesses are Celestia, Luna, Cadance, and Twilight Sparkle, and if Celestia really had a daughter, he's sure she would have mentioned her. Outraged, Sunset says she only knows Twilight Sparkle as Shining Armor's little sister, and she's no one of consequence. He starts thinking and then briefly loses his temper upon realizing Sunset's definitely not lying and he's in another dimension again, firing a Uranium Ray into the sky. He calms down and introduces himself. Based on everything she's said, he's not where he's supposed to be.
In a tent at the front of the Nightmare Army is its leader, the 1020 year old vampire pony Countess Mircalla of the Crooked Peaks. She grants an audience with Bagan's minion Mizu, the sea monster. It looks like a mass of darkness vaguely in the shape of a largely indescribable aquatic creature, with glowing blue lines running through its body and a blue jewel in its forehead. Despite being a vampire from a snow capped mountain range, Mircalla feels cold around it and its presence creeps her out. It communicates telepathically and has been supplying the army with strange weapons and devices, like the summoning pedestal Sunset Shimmer destroyed. The army has Nightmare Moon's old breastplate armor, still full of dark energy and Mizu requests to see it. Mizu charges the armor with energy and repairs it. It communicates its plan, which involves Mircalla donning the armor and taking on Nightmare Moon's powers as extra assurance until they can get the armor back to Luna. Mircalla weighs her options, unsure of whether to trust this strange being, then accepts. Now taking on a form similar to Nightmare Moon, Nightmare Mircalla stands in the sunlight for the first time in over a thousand years and laughs. By the time this is over, it will be the last sunrise the Equestrians ever see.
