So if season 2 ended differently... THIS STORY!!! Have fun seeing Chrysalis take the reigns from season 3 and beyond. At least my interpretation of what she would do.

“You won’t get away with this, Twilight and her friends will-"

Cadance’s defiant words were interrupted as the main doors burst open. The six mares who failed to obtain the Elements of Harmony were dragged into the grand hall, which was in partial redecoration, and sported a large amount of changeling slime. The six ponies were closely escorted by just as many changelings.

With a snide smile, Chrysalis turned towards Cadance in a tone that revelled with smugness as gooey as melted caramel.

“You were saying…”

The frazzled pink alicorn's widened her eyes in dismay. The element bearers were still on edge, they battled between discouragement and defiance in their expressions.

The queen struck a dramatic pose as she faced her newest prisoners. Chrysalis stared down at Twilight Sparkle specifically.

“You do realize the reception has been canceled don’t you!”

The giant of a changeling then turned to her smaller subjects, who hovered anxiously in the air. They growled and hissed in anticipation for the expected orders.

“Go! Fee-, wait no,no,no, I’m forgetting something aren’t I.”

With a bright flash of green magic, a roll of old parchment appeared in front of Chrysalis, as well as a small pair of reading glasses. It unraveled as she put on the glasses, and her harlequin eyes peered through the list on the paper. She thoughtfully rubbed a fetlock under her chin while she scanned through it.

“#34 yes, #35 yes, #36 yes, #37... business before pleasure. Ah yes, I can’t let every changeling go free form until the plan is sealed. Wrap up the Element Bearers. The would-be bride and her husband need a more permanent holding as well. Cocoon them all.”

A large holed hoof was lazily gestured towards the prisoners, and the queen’s entourage of servants quickly obeyed. With a mixture of magic and coughs, mounds of slime were produced and used to encase the prisoners in fresh cocoons.

Fearful yelps and wails of despair escaped the colorful ponies as their future was sealed in green goo. Chrysalis chuckled at the particularly furious glare Twilight gave at her.

“You can’t, you won't ge-"

Twilight’s words were interrupted by a glob of green goo being slapped on her muzzle. The queen carried on in a dismissive tone.

“As much as I’d like to entertain your pathetic little struggle, I have grander things planned.”

One grapple of magic later, the little purple unicorn was shoved into a green viscous cocoon, and closed in. This was followed by the yellow, blue, orange, pink, and finally the white pony. Each of which were properly gagged with slime to prevent any last retorts of defiance or cries of despair.

The imposing changeling monarch turned to the not so happy couple at the podium, and walked up to them until she was a step away. Chrysalis stared down at defeated peachy princess. The grin on her fanged face was fastened securely.

“Thank you for the disguise. Have sweet dreams on how things could have been.”

“You EVIL WI-"

-gag-

“Tsk, Tsk. Now that sounded like you were going to use uncouth language, so unfitting for a princess... or any new subject of mine. From here on out there will be consequences for defiance. You’ll be one of my prime examples...”

Seized in magic, the smaller alicorn was violently torn from her goo cemented position, and packed in like jelly in a donut, albeit a cocoon instead. The queen then turned to Shining Armor, delicately running a hoof down his masculine jaw.

“You’ve served me well, but now your fountain has run dry, farewell Shining.”

The once proud captain of the guard walked over to a prepared cocoon, and crawled into it. Once inside, Shining used the last of his magic to seal himself inside. A stupid smile bedecked the unwitting victim of mind control. This caused a sadistic chuckle from Chrysalis.

“Now time to double check if there is anything else I’ve forgotten. Are there any particularly stubborn pockets of resistance Shade?”

A spotted changeling vanguard stepped toward his victorious ruler, and bowed low. His purple eyes distinguished him as the head of his division.

“The princess of the night is holed up in her tower. We found her asleep, but when we tried to enter her chambers some kind of alarm went off. Once awake she proved too difficult and wily to subdue. However, I made sure that every angle has been cut off. Including any potential underground tunnels. Also a teleportation nullifying field has been cast and is being maintained by many of my vanguards. We might not be able to subdue her, but at least she won’t be making any conventional escape by magic.”

“Of course, Celestia’s unstable sister, bring the rest of the vanguard and some sentinels. I don’t want there to be any chance of her escape.”

Chrysalis then turned to her freshly minted prisoners. Her hoof thoughtfully tapped at her chin as she mulled over a few additional thoughts. It didn't take long for her to come to a decision. The Queen's long legs brought her over to where the Element Bears lay trapped, the Princess of Love and of the Sun lay wrapped, Chrysalis's mouth was wide open as they all were sapped.

If Shining Armor's love was enough to throw Celestia off her game, then Cadances', the Element Bearers, and Celestia's own positive energies should be more than enough to subdue Luna.

As the Queen engorged on more emotional power Shade acknowledged her command and cast a practiced spell. The vanguard’s eyes glowed a fiery purple as a wave of transparent energy blew out from his horn.

“The message has been sent my queen.”

“Excellent, Vivisect call in the sentinels, no pony will free my prisoners. Once my city is secured all changelings will feed at their leisure.”

A particularly large changeling specimen covered in extra-thick chitinous armor stepped forward, acknowledging her queen's command. Without another word Vivisect’s eyes glowed orange while she called other sentinels to the grand hall. Once the message was sent the burly changeling rose and uttered in scratchy voice

“The sentinels will be here shortly my queen.”

“Good, I will personally put the last princess down"

Chrysalis licked her lips for emphasis, reveling in the hype of energy she enjoyed. Truly there was nothing like this. Never before did she have access to such ponies with so much potential. She had to consciously keep herself from trembling, for she felt that with this much power she could explode... Exploding could wait though, she still wasn't quite done with formal business. She turned to her head vanguard, trying to keep her composure somewhat regal.

"Shade, come.”

The room tittered and buzzed as excited changelings and their Queen hovered out of the wedding hall. A broad grin couldn't keep itself off of Chrysalis's muzzle as she led the charge out the balcony window. The opening briefly flooded with black chitin and transparent wings.

The swarm of the queen and vanguard flew across the city toward the Lunar Tower. As they passed a screech of cheers came from the chitinous legions of changelings below. Their disturbingly synchronized sound sent a shiver down the pony population’s collective spine. The scene of victory filled Chrysalis with joy and giddiness. She had planned this day, even though so many fears had plagued her in her preparations. However, the scene below made her throw out any doubts as to whether these plans had been worth it.

Chrysalis began to laugh. As her eyes roamed over city street to city street her laughs escalated. Each scene was a validation of her superiority. Eventually her raucous laughter started to interrupt her flying to the point she felt light headed. After a particularly wide and unruly swerve, the head vanguard raised his voice in concern.

“My queen, are you faring well?”

Shade asked, offering a hoof for support. She gently brushed the offered hoof aside as the booms of her laughter died to chuckles. Though she did clutch to her sides in an attempt to massage her overused muscles.

“No Shade I’m am quite fine. My enthusiasm just got ahead of me.”

“Well, the Lunar Tower is just ahead.”

“So it is.”

The queen and her elite band hovered in front of the structure. The tower's head was completely engulfed in impenetrable darkness. Tendrils of ominous shadow guarded the fearsome abyssal structure. Dozens of vanguard changelings already surrounded the tower. Each of them contributed to transparent green barrier, which surrounded and blocked all angles of the nightmarish edifice.

“Hmm, Shade go fly into it and find out what that darkness does.”

The head vanguard flinched at the idea, there were many rumors of ex-Nightmare Moon, or Luna rather. Those rumors gave sufficient cause to fear the Princess of the Night. Yet his Queen had commanded so the head vanguard steeled himself. If his queen commanded, he would obey, so he began to fly forward. Shade’s advance was stopped by a large hoof to his chest, he looked up to see Chrysalis stop him from obeying her own order, his muzzle scrunched in confusion. She laughed one more time in jest.

“I was joking, there’s no need to risk your chitin when I'm here. Get the other vanguards to reinforce my position.”

The Queen gave her smaller subject a pat on the head and ruffled his neck fin a bit. Shade sighed in relief, Chrysalis's sense of humor was a quite turbulent, even after years he'd never really gotten use to it. He relayed the order and spread out with the rest of the vanguard. Their optimal positions were nearby the Queen, so they could add their magical reserves to hers.

Dozens of the prepared vanguard stayed a good distance away, doing the important job of maintaining the Teleportation Nullifying Barrier. The Princess would not simply blink away from this situation. Chrysalis turned towards the tower, casting a spell to amplify her already reverberant voice. The Royal changeling resonated with the thunder of a mocking crowd.

“Come out, come out Luna. This transition will be less painful if you surrender quietly.”

The cacophonous words blew away the air around the tower and tendrils of shadow whipped about like the branches of a tree. Chrysalis patiently waited for a response, when none came forth she graced Canterlot with more rancor.

“I’d rather not damage this beautiful tower, but I will, if you don’t come out, NOW!!!”

Chrysalis’s jagged horn began to glow with baleful energy, as she readied to blast the top of the tower away. Before any energetic green carnage was released, the shadows that surrounded the tower started to coalesce. The darkness condensed around a figure, who stood on the balcony of the tower. It never solidified enough to reveal the mysterious figure who stood there however. Chrysalis’s horn stayed charged as she addressed the new predicament.

“Very good Luna, now there’s a room calling your name up at the wedding halls. I'd like you to quietly check-in.”

The vanguards that surrounded the queen snickered and jeered at their leader's taunts. Among the darkness a small glow appeared in the center, turquoise eyes with slit pupils gazed out of the abyssal wave.

“Do not address me as Luna fiend! If thou desirest a fight, you will face the Nightmare!”

The shadows solidified into a tall armored black alicorn. Nightmare Moon reared onto her hind legs then stomped down with her front, shattering the front of the balcony. Pitch black clouds spewed from the top of the tower, and darkened the sky. Lightning cascaded across the clouds, and threatened to fry airborne changelings.

Many of the vanguard gulped, succesfully intimidated by the chilling display. Honestly Chrysalis was a bit spooked as well, but then she shook her head. Things were different now, things were very different now. She had just beaten CELESTIA! The scales were tipped in her favor, she had to remember that. Though years of feeling inferior to these demi-god sky ponies took a few moments to subdue. When she collected herself she tried to show her confidence with a good coating of smugness.

“The elements took your edge away Luna, you can stop pretending you’re that fearsome.”

The black alicorn blinked in surprise and took a step backward, but Luna wouldn’t let the queen call her out so easily.

“Then taste our power curr!”

Pale blue energy exploded from the spiral horn on Luna’s forehead. Prepared for the aggression, Chrysalis answered with her own emerald ray of power. The two cataclysmic surges collided with violent impact, and an echo of shock reverberated across several of the city blocks. Nearby windows shattered under the intensity of the sound. The queen grunted under strain required to maintain the spell, and she didn't know how manageable her new levels of power were and she didn't feel like gambling, so she shouted at her soldiers.

“Flank her!”

The unit of Vanguard obeyed immediately, adding their own blasts against the dark alicorn. Luna was struggling to maintain the energy wrestle from the start, so when Chrysalis's support pepperd her sides she folded quickly

The Nightmarish facade vanished and Luna was thrown bodily back into the tower chamber. Chrysalis didn’t wait a moment to follow up on her attack, she dashed into the night tower and landed with a stomp inside of Luna’s personal chambers. Her vanguard followed shortly after.

The circular room reflected the night sky, and stars slowly moved across the walls and ceiling under some magically aesthetic force. A large moon was centered at the apex of the dome shaped ceiling. Though the changeling queen took only a moment to glance at the details, after all she could take all the time she wanted to admire its beauty later.

Luna lay in a mess on the floor, sizzling. She had hit a few book shelves and their contents were splashed all over the floor. The blue princess was smoking, bits of fur still glowing with small embers, and her horn had darkened scorch marks, enough to match the ones Celestia had recently acquired.

Chrysalis stepped with self-assured confidence next to the fallen Princess of the Night, and proceeded to place her large hoof on Luna’s horn. The beaten alicorn flinched under the sudden pressure on her sensitive, freshly burnt appendage.

“I told you a quiet surrender would be less painful, but you had to spite me.”

Chrysalis leaned into her hoof, increasing pressure and causing a hair-line crack in the alicorn's horn. Luna’s eyes shot open and she gasped in shock and pain. Eventually the queen lifted her hoof off the horn, before it could break. Then she made a lethargic gesture at her Head Vanguard, indicating the fallen Night princess.

“You know what to do Shade.”

“Yes my queen.”

“Also send for Colony, I need to establish some ground rules about our open feeding season. Tell her to meet me in the throne room.”

“It will be done.”

Shade turned to a fellow soldier and clicked a few times. The subordinate nodded before it flew out of the Lunar Tower. A long yawn escaped from Chrysalis’s fanged mouth, she raised a hoof to politely cover it. The beat down on Celestia and Luna had been tiring, even if she had all the magical energy she could want. The mental stress of it all resulted in substantial anxiety fatigue. So she moved over to the giant lunar bed, which was several pony body lengths wide and deep. The conqueror lazily flopped onto it, stretching out and slowly caressing one of the fuzzy blue pillows. She hummed with delight.

“oOOo, how exquisite. I think I’m going to like it here Shade. It feels good to finally be in my own skin in civilized society. I think my chitin will finally get the treatment it deserves.”

Shade worked to put Luna into a fresh cocoon, and shoved on her backside with a hoof. He paused to grunt in agreement with his Queen, then shoved on Luna with extra heft. The princess made a sloppy noise when she slammed into the slime. Muffled whimpers could be heard from the captured alicorn, who cradled her horn even while she floated in the semi-viscous fluid. The vanguard commented even as he sealed the Princess away.

“Pony establishments could hardly treat us worse than the filthy and perilous Badlands.”

“Indeed, that also gives me an idea, I don’t remember the last time I had a real bath.”

Chrysalis tilted her head and stopped feeling the pillow. She looked down at the fuzzy head rest and could see she had already smeared some of her accumulated filth onto it. At first she frowned, then an idea came to her and a wicked grin crossed her features.

“Hmm, I’ll have to see what Celestia used to clean her royal hiney”

She echoed deep mirth across the Lunar Chamber. With some regret she hoisted herself from her comfortable position on the night themed fluff of luxury. She needed to talk with her Head Drone and see that her prisoners were securely put away. Then she could indulge in some of the comforts these ponies pampered themselves with.

With a buzz of her wings she exited the Lunar Tower, closely followed by the remainder of the vanguard and their neatly slime wrapped prisoner.