Transformers: Harmony and Chaos (?omplete?)

The Autobots, and ponies look on, bewildered, that the changeling queen, has become a perfect double of the Autobot leader. Even her voice was down to the T.

"Prepare to be destroyed!" The doppelganger Prime yelled out in an unsettling sound, as the others are so used to Optimus' benevolent spirit.

"Not while I still function!" The real Optimus says as he charges towards his clone.

Both Primes turn their right hands into orange energy axes, and begin fencing with each other.

"Twilight," Bumblebee says to the unicorn, "I think this might be the best time for you to look for the Elements."

"Right Bee. You heard him girls! Let's get going." Twilight addresses the others.

All the ponies nod in agreement, and begin to charge towards the back chamber where the Elements of Harmony are held.

On their way, however, they see more of the strange green cocoons, and multiple changelings guarding them. The moment the changelings saw the ponies, they swooped over to engage.

Once again, the ponies use their skills, bucking, magic, staring, party cannons, to force their way to the doors that held the Elements.

Back at the battle with Optimus, and Chrysalis Prime, Ironhide and Bumblebee watch in confusion. The two Autobots have already lost track of who is the real Optimus, and who is the Queen.

One of the Primes delivers a roundhouse kick to the side of the other. The other Prime retaliates, by hammerfisting the opponent in the chest. The blows were brutal, and multiple strikes were landed by both combatants. 

Their fists collide with each other, and then their guns go ablaze, as they try to fill each other up with laser fire.

"I can't tell who's who!" Bumblebee yelled out.

"Well all we can do, is watch until we figure somethin' out little buddy." Ironhide replied.

Back with the ponies, Rainbow Dash slams one of the changelings so hard, it flies into one of the cocoons. It begins to crack, then crumbles. Inside, was a blonde maned, and grey pegasus. The pegasus opens her eyes, revealing them to be crossed.

"DERPY! You OK girl?" Rainbow asked with concern.

"I'm fine, thanks Rainbow Dash. I felt like my emotions were being drained when I was in that thing."

It then hit Rainbow Dash. The cocoons, they WERE the missing ponies! Chrysalis had captured the ponies, encased them in cocoons, and was draining love energy from them. It was the source of her power.

"Twilight!" Rainbow yelled to the unicorn, "Destroy the cocoons! The missing ponies are trapped inside. The changelings are draining the love out of them literally!"

Twilight and the others hear this revalation, and begin attacking the cocoons, as the changelings tried to stop them.

Applejack was more determined than any of the other ponies. Now she knew where to look for her brother and sister, she began bucking every cocoon she could find. She had already broken a couple open. Applejack had freed several ponies she recognized as locals in Ponyville. The were Lyra, Bon Bon, Dr. Hooves, Caramel, and even the grouchy Cranky Doodle Donkey. They all thanked her as they tried to look for a place to escape.

Twilight realized there's no where for the escapees to go.

"Sorry about this Princess" she says to herself, as she charges up a large blast, and blows away a section of the wall, creating a large hole that leads out of the castle.