“Stand back! It seems I have another resurrection to perform.” Grogar drew sigils in the dirt as Tirek, Chrysalis, and Cozy Glow obeyed. A golden bubble grew out of the ground to encompass the symbols, large enough for a pony to stand inside.
“What is--” a flash of energy knocked Cozy Glow into Tirek’s shoulder before she could finish her question. The centaur swatted her away as the bubble filled with curling black smoke. Grogar looked on, frowning.
A glowing pair of eyes opened within the smoke. “Crystalssss….”
“Well, hi there, Sombra! Welcome back!”
“King Sombra!” The encapsulated shadow hissed, whirling to face the pink filly. A pause. Then, “Why have you brought me back again? Ha! You need me after all, do you, Grogar? Of course my powers are indispensable to your plan to conquer Equestria!”
“I do not need you; I could merely make use of you if you will agree to cooperate.”
“If you say so,” chuckled the shadow, and it solidified into a smirking gray unicorn.
“It is you who needs me, Sombra, or have you forgotten who has resurrected you twice now? You have proven that you cannot defeat the ponies on your own, but if you insist on mocking me I will return you to the aether and demonstrate to these other expendable second-rate villains just how much I do not rely on any one of you!”
Somewhere, a single drop of water freed itself from a stalactite and the plink of its landing echoed through the lair.
“Join us, Sombra! We could use another pony on this team! You and I could be best-pony-villain buddies!”
At that prospect, the King blasted the impervious bubble prison with magic, bucked and pushed and struggled to no avail.
“My offer to grant you rule over a portion of Equestria in exchange for your promise of loyalty still stands,” snorted the goat. Sombra shot a threatening glance at Cozy Glow over his shoulder before squaring himself into a dignified, kingly stance.
“I accept.”
“Since you have already appeared to the ponies, Sombra, you have volunteered yourself as the face of our operations for the time being.” Grogar stalked around the table where his questionable allies reclined. “It will be to our advantage to have our league go undetected as such for as long as possible.”
“A most agreeable suggestion, O Grogar – punish the delinquent by making him do all of our dirty work!” Tirek sneered.
“Or Chrysalis, disguised as Sombra!” In response, the Queen gave Cozy Glow a whack that sent the filly tumbling across the table.
Sombra caught Cozy Glow in his magic and proceeded to toss her away to the edge of the room. “I have a suggestion! A plan for our first move against the pony throne,” he declared.
“You forget who is in charge,” Grogar leaned into Sombra’s face and got a frown in response.
“Nevertheless, I believe you will find my suggestion most advantageous, and I will even agree to carry it out for you.”
“Out with it then, if you insist on telling us!”
“It may have been Twilight and her friends that last defeated me, but upon reflection I have realized that they were only able to do so with the aid of Discord. His power appeared to match my own as long as he wasn’t distracted, and for this reason I think we would do well to ensure that he takes no role in the defense of Equestria. We must eliminate him from the conflict to come.”
“Ha! You would take down Discord? You said so yourself that he is as powerful as you are.” Chrysalis chuckled.
“He is not! But he has revealed his weakness. I distracted Discord enough to injure him by aiming an attack at the pony he declared to be his favorite. If we kidnap--”
“If you kidnap,” Tirek interrupted.
“If I kidnap that pony and hold her hostage, Discord will agree to stay out of our way in order to protect her!”
“Hmm.” The goat paced around to the head of the table where his Seeing Eye sat and conjured in it imagery from Sombra’s most recent defeat. “I like where this is going. The chaos lord does appear to be sincere in his declaration of attachment. You kidnap the pony and appear before them all holding her as a hostage. In exchange for her safety, Discord promises not to intervene, or if he doesn’t promise, we kill the pony right away. In either case, Twilight and her friends will be missing an element and likely unable to perform their most powerful magic.”
“Not to mention how discouraged they’ll be to see King Sombra back again, after they already defeated him twice! Just imagine their faces!” Tirek erupted into uproarious laughter, to which Cozy Glow added her own shrieking giggles.
“QUIET!” Grogar stomped. “I have made up my mind. Sombra, you will kidnap the pony tonight. She lives in this cottage,” a small house abuzz with animal life appeared in the Seeing Eye. “And you can enter and exit through the Everfree Forest to remain unseen. Chrysalis! I will use your magic of disguise to fortify this lair with a cloak that should keep our activities undetected. Tirek and Cozy Glow, just stay out of my way until I know enough to issue more orders. Are we all understood?”
“Oh, yes, Grogar, of course we are, but, um,” Cozy Glow seated herself in the center of the table. “Just one, teensy little question. What are we going to do with the hostage once we have her? She’ll need to be kept somewhere out of earshot of all our masterful planning, and of course she’s just a mortal pony like me, so she’ll need to be taken care of in order to be kept alive you see, and...”
“Very well,” spat the goat. “You shall supply her needs, since you as a mortal pony will understand them best, and I have a room in the crypts beneath this fortress that can be altered to hold the prisoner.”
“Golly, that’s just great! Except I am not having anything to do with that pony! She was one of the teachers at the friendship school, and have you seen those big, sappy eyes of hers? Why, she was almost as good as me at guilt-tripping! I just hate to be challenged!” Steam rolled out of the filly’s ears. “So you see, I really can’t be trusted with the care of that pony.”
Grogar lowered his face into his cloven hoof and pushed out a heavy sigh.
Chrysalis stood up at her seat and pointed across the table at Sombra. “Why not make him deal with the prisoner? Taking a hostage was his idea after all!” Predicting an argument, Tirek grabbed himself a handful of recently-conjured popcorn.
“What?” Sombra took his turn to stand. “I only agreed to capture the pony! I will not put myself at her beck and call to attend to her frivolous mortal needs!”
“I’ve had enough of this bickering!” Grogar stomped a second time. “Sombra, you will be solely in charge of the prisoner, both her care and her interrogation. After all, it may be best if not even she knows of our league. Now,” he stood, “prepare yourself for your assignment; carry it out tonight and do not fail me. Chrysalis, come, we will erect our defense.”
The sound of hoofsteps retreated in two directions down the corridor and quiet fell over the table where Tirek and Cozy Glow still sat.
“So,” the filly began, “shall we—”
“No.” Tirek’s chair scraped the stone floor as he stood and soon there was another set of retreating hoofsteps.
“Aw, horsefeathers.”
This was enjoyable, so far. There are several things here I have to give you praise for. First, the overall presentation turned out very well. The way you describe scenes and the actions and movements of the characters makes this story feel a lot like the show. It can be seen that you studied its style quite well.
Second, you write all of them in-character. I am especially impressed by your portrayal of Grogar and your portrayal of Fluttershy. Grogar's wit when he chose Sombra to take care of Fluttershy so that she won't find out that there is an entire team of villains instead of just him (I was thinking that's what Grogar should do, in case Fluttershy somehow manages to flee, and just a few sentences later, he actually did this and I was astounded to see that!) and Fluttershy's quick switch from being fearful to using her abilities to prevent Sombra from raping her, these were both magnificently written.
Not all new pony authors do the characterization well right from the start. There are only two scenes where a character's behavior feels off, which I'll come to later. You have a knack for writing them all.
And third, you have all the villains do the exact right things. I already mentioned Grogar and his wit, but Sombra and his strategies to keep Discord at bay work just as well. I was wondering if Discord shouldn't be able to get ahold of the situation easier; since he could feel the magical disturbance in the throne room when the projection of Sombra and Fluttershy appeared, he should be able to trace Sombra's magic back, too, and then teleport there and free Fluttershy with a snap of his claws before Sombra can react. But finding a believable reason for it why Discord doesn't fight a villain isn't an easy thing for a MLP: FiM fanfic author to do and since you're a new author, this can be overlooked. And you still did your best and showed a great amount of effort to find such a reason, by having Sombra not being physically present.
You came up with a pretty good, flawless plan by the villains here and it's going to be very thrilling to watch how Twilight and her friends are going to deal with this.
There are a couple more things I noticed that I want to address. Since you're a new pony author, I will take the time and go through them thoroughly. I'll make a comment for each chapter, to make ít easier to go through it all.
This is one of the behaviors that feel a little out of character. Tirek did not appear like he would worship Grogar in the show. It was seen that he has a certain amount of respect for him, but especially considering that he has started to backstab him together with Chrysalis and Cozy, it is unlikely he would refer to Grogar with "O Grogar".
The second one is this reaction by Cozy:
The problem I see here is that Cozy gives up too quickly. Whatever she wanted from Tirek (which would be nice to know, there are dozens of possibilities, after all), if he says no, it would be far more in-character for Cozy to pester and annoy Tirek until he changes his mind. She gives up uncharacteristically quickly there.
But, since this story is an Alternate Universe story, this might have been your intention even, to characterize Tirek and Cozy slightly differently, in which case you will probably explain the different personalities at some point.
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I was imagining how Tirek had bowed to Discord in the show when the former was first introduced. Tirek knows how to feign submission when he realizes he's in a weaker position, so I was trying to channel that a little in my story. The "O Grogar" bit is meant to be exaggerated, where Tirek is trying to establish a dichotomy between himself and the "delinquent", Sombra.
Having received the command from Grogar to basically sit tight, Cozy Glow was about to propose some sort of game or bonding activity to do with Tirek. He had sensed it coming and immediately denied her. I suppose an argument could be made for Cozy to pursue him, but since she didn't actually have anything pressing to say and since he was clearly not willing to play a game, I chose to have her stay put.