There were many other dimensions beyond the one Equestria was in.
A magic-less world inhabited by humans instead of talking ponies.
A dimension inhabited by miniature flying ponies called Breezies.
A hell dimension called Tartarus where monsters were imprisoned, rumored to also contain souls of the damned.
A chaotic dimension inhabited by an all-powerful draconequus named Discord.
A parallel universe where dragons weren't lavaproof.
A timeless dimension called limbo.
And a world whose light had been devoured by two dark spirits, who were seeking a new world to feast on. They were creatures called symbiotes, who could merge with a pony. The ponies would be dominant, but under the influence of the symbiotes, who didn't care what the ponies did as long as they did something evil to the world.
In this world, the two symbiotes met up at an ancient ruin.
One was a cloud of dark blue smoke. The other was a cloud of black smoke. They took the shape of ponies, with glowing eyes.
They had just had an opportunity to influence a pony who had crossed into their world and missed it, for the pony had been rescued by her older sister, despite the attempts of the tree golems who served them.
"It's such a shame that Luna left," said the blue symbiote in a sinister female voice. "If she let one of us in, she could become a great threat to Equestria."
"All in due time, Nightmare," said the black symbiote in a menacing male voice. "You felt her resentment towards her sister."
"They might be on better terms now, Shadow," said Nightmare. "After Celestia rescued her."
"Sooner or later that resentment will come out again."
"You may be right. I could feel the jealousy deep within her as I spoke to her. They are to rule Equestria together, and there is a good chance she might feel overshadowed by her. Maybe she will return to us."
"And once you're inside her, you can influence her to open a portal and let me into Equestria to find another pony."
"Perhaps. But I think there is already a link between our world and Equestria."
"Do tell, Nightmare. Where is it?"
"At this very ruin. After Luna crossed over, I sensed an energy emanating from the lowest part of the ruin similar to the portal she came through. I think it's connected to somewhere in Equestria."
"Show me."
Nightmare led Shadow into the ruin, and down a flight of stairs.
"Stairs," said Shadow. "For some reason I get an evil vibe from stairs."
"Perhaps there's some evil pony in Equestria who's obsessed with stairs," said Nightmare. "Or will be. We're here."
They reached a dark underground temple-like room.
"Here," said Nightmare. "I can feel Equestrian energy on this wall."
Shadow tried to cross through it. He couldn't. Nightmare did the same.
"It appears we cannot cross into Equestria through here," said Nightmare, pointing out the obvious.
"But wait," said Shadow. "I can see the temple on the other side of the wall. Hmm. The Well of Shade, it's called. I believe we can cross over if we can merge with a pony on the other side."
"What pony would go there?"
"Probably just the type of pony we need. One seeking power above all else. I think we will be able to communicate with them."
"What about Luna?"
"We sensed the last time she opened a portal from Equestria. If she opens another one, we'll know. Until then, let's wait for a pony to come to the Well of Shade."
So, they waited on the dark side of the Well of Shade...
Quite some time later, the symbiotes caught sight of a skinny unicorn entering the Well of Shade. He did not look very happy at all. Shadow and Nightmare read his mind as they had done with Luna. He had been cast out by the Pillars of Equestria when they mistakenly thought he was trying to steal their power, and he resented them for it.
"Perfect," Shadow whispered to Nightmare. He then spoke to the unicorn. "Stygian!"
"Who's there?" said Stygian. So, he could hear Shadow from the other side of the wall.
"A being of great power," said Shadow. "We can give you power beyond any you could imagine."
"I'm listening."
"All you have to do is let me in. When you do, you will be more powerful than the Pillars of Equestria. More powerful than any unicorn in all of Equestria."
"Yes! Give me your power!"
Shadow flowed through the wall and into the Well of Shade, entering Stygian through his mouth and ears.
"Now, to get revenge on the Pillars!" Stygian ran off.
When Stygian returned to the Pillars to confront them, his eyes turned black, a cloud of darkness appeared around him, and he mutated into a giant black alicorn.
Their transformation was complete. Shadow and Stygian had become one. They were now the Pony of Shadows. And, once he'd gotten revenge on the Pillars, he'd bring eternal darkness.
Nightmare waited for another pony to appear. But, for a while, no one did, and she began to lose hope.
She wondered why Shadow... no, the Pony of Shadows... hadn't opened a portal between worlds yet. Had he been destroyed? Or banished to another world? Was his power not enough to defeat the Pillars of Equestria?
Nightmare kept waiting at the temple, sure another pony would come sooner or later.
One day, she suddenly sensed a portal opening from Equestria. She was sure she knew who it was. She flew to the portal as fast as she could.
Princess Luna stood in front of the portal that had opened up. Nightmare could sense a powerful jealousy emanating from her, and it tasted so delicious.
"So, Luna," said Nightmare. "Have you finally decided to embrace your darkness and become more powerful than Celestia?"
"I have," said Luna. "The ponies all play in her daylight, and sleep through my beautiful night! I will not stand by any longer. I need more power to overthrow her."
"Well, you've come to the right place. One little word is all it takes."
"Give me your power."
Nightmare entered Luna through her mouth and ears. Like Stygian, she did not change right away.
"Did you really expect me to sit idly by while they all basked in your precious light?" Luna said to Celestia, back at their castle. "There can only be one princess in Equestria! And that princess will be me!"
Luna raised the moon over the sun. A cloud of darkness appeared around her, glowing bright red. Luna's eyes turned into slit pupils. Her teeth became fangs. She grew to Celestia's size (much smaller than the Pony of Shadows), her coat black instead of dark blue.
The fusion between Nightmare and Luna was complete. They had become Nightmare Moon.
Author's Note
Since Legends of Magic seems to actually fit in better than most of the other comics, the story was based on Issue 1, and the episode Shadow Play. A little bit of headcanon backstory on Nightmare Moon and the Pony of Shadows, and how they came to be.
I initially thought there were three symbiotes in the Legends of Magic comic, but I think those eyes and mouths belonged to the golems.
