POV: Princess Twilight Sparkle
Four Days after Princess Luna’s infestation...
It has been a week since the alliance with the Zerg was established and something seems off about Princess Celestia and Princess Luna. Both of them have begun to act... strange ever since Princess Celestia returned from her military expedition into the Everfree.

At first it was subtle, with the two of them now seemingly able to read each other’s thoughts during war council meetings, somehow knowing where each other is even if they were told no such information, and they were also beginning to eat less.

Now, its much harder to ignore. They have started sending soldiers to the Zerg base for seemingly random reasons, allowed the Zerg ambassador to join them in war council meetings multiple times, and have even begun switching shifts in raising/lowering the sun/moon.

The last one was what caused me to notice these things. I had already gone to both of them multiple times to ask what was going on, only to be ignored or given a vague answer.

Now I’m growing more and more concerned despite their repeated attempts to assure me that nothing is wrong. It has now gotten to a point where I don’t know who to trust anymore.

This is reminding me of my brother’s wedding, where I knew something was wrong even though everyone said things were fine, only to be proven correct when Queen Chrysalis invaded with her Changelings.

But instead of only one pony being replaced, it feels like nearly everyone that comes in contact with the Zerg change in some way...

POV: Simon
My brood has grown significantly since we infested the two ruling Princesses, with my ground army now coming in at one-and-a-half thousand Zerglings, five hundred Hydralisks, two hundred roaches, fifty Ultralisks, and twenty-five Infestors.

My air force may be smaller by a wide margin, but it is still more than enough to guarantee air-superiority. With one hundred and fifty Mutalisks, sixty Corruptors, fifty Overlords, and twenty Overseers under my control, I have nothing to fear from any air force that might challenge the swarm.

I have also given myself Carapace armor, covering my chest and legs while leaving my arms untouched as to allow me continued use of my C-10 Canister Rifle without difficulty.

“Drone four, progress on Equestria’s infestation.” I had left my ‘ambassador’ with one hundred of my advanced neural parasites and told it to only infest the most important targets.

“We have infested the two ruling princesses, the captain of the Lunar and Solar guards, and twenty royal guards.” The Drone answered. “In addition to this, we have nearly every member of the Equestrian war council, and many other high ranking officials under our control.”

“What do you mean ‘nearly every member’?” I asked after taking a moment to analyze the information. “Who among the Equestrian war council is still not under our control?”

“Princess Twilight Sparkle, my lord.” The drone replied. “She has been cautious to have somebody with her at all times, making infesting her without being discovered impossible.”

“Shit, she’s the biggest threat to the brood when she is with her friends.” I swore out loud before I began formulating a plan. “I will have Celestia seek to talk with her alone in the gardens, you burrow there and wait until she walks past before infesting her.”

“It shall be done.” Drone four replied before removing itself from the hivemind once more.

“I must make sure the Equestrians have no chance of victory, just to be safe.” I thought before returning to managing my base.

POV: Princess Twilight Sparkle
I was suspicious when Princess Celestia asked for me to speak with her in the royal gardens alone, but I would never deny my mentor’s request for a peaceful conversation.

“I have come to warn you.” I jumped around to see the Zerg ambassador floating behind me. “My lord has ordered me to infest you with a neural parasite that would force you to obey his commands.”

“And why are you telling me this?” I asked my foe as I readied a fireball spell. “I thought you would just obey the order without question.”

“I follow the strongest leader, and I sense that you have the strength necessary to lead the Swarm.” The drone answered before it a gesture that was essentially the equivalent of bowing down to me. “Your psionic potential is unmatched and Celestia considers your spellcasting skills second to none.”

“How do you know that?” I asked the Zerg drone as I canceled my spell.

“My lord has already infested your princesses, as well as multiple important figures in your society.” The drone answered, confirming my suspicions that something was wrong. “They are most likely on the way here now to ensure you have been enthralled.”

“What are we going to do now?” I asked the drone while trying to the fear in my voice. I knew that fighting my former teacher and friend was something I could not do.

“We run.” The drone answered moments before a possessed Princess Celestia spotted us and charged.

POV: Simon
I watched furiously as Twilight Sparkle and the traitorous drone fled from my thralls. I couldn’t channel my psionic powers through them since they were not Zerg units, meaning I was helpless as the two escaped from my forces.

“Celestia, your student has joined the Zerg, she is now an enemy of the state and must be apprehended.” I psionically influenced the Solar Princess thoughts while dispersing my gathered minions.

After I had finished mind-wiping those who didn't need to know of Twilight and the rogue Drone's team up, I returned my focus to growing my army. I knew that with Twilight being branded as a traitor, she would be unable to gather allies from Equestria.

POV: Drone Four
As we escaped from my former master's units via a teleportation spell, I knew that I would no longer be accepted by his brood, which I deemed as an acceptable loss if it meant I could serve a stronger leader.

"What now? Simon would already have had the Royal Guard begin searching for me." Princess Twilight asked me as we moved to get as far away from Simon's forces as possible.

"I have a plan, but it will require three things." I answered as we traveled through the jungle, the native wildlife knowing that I was of the Zerg and thus keeping their distance.

"Which are?" My new master asked before I linked her into my hivemind frequency so we could communicate more efficiently. "Ow! Please warn me if you are ever going to do that again."

"Apologies, I needed to do that so I could transfer all the knowledge you would require to understand my plan." I then began to slowly give her the information of my plan and what it required, which was a supply of essence, a safe place, and some time.

My plan was to create an entirely new brood, one under Twilight's command, so she can properly combat the Phantom Brood. Of course, it means that I must sacrifice myself to create the hatchery that will become her headquarters.

A fact that Twilight was not happy with...

"If you turn into a Hatchery, who will help me do this?" I could sense the distress in Twilight and used our hivemind to calm her down. "I have little-to-no experience leading anybody, much less an army of Zerg!"

"My memories and mutations can transfer over to any drone you create." I said to the Alicorn. "I will also become one with the hivemind once I mutate into the hatchery and will be able to guide you even if my form were to be destroyed."

"Where do we start then?" If I had a human mouth, I would be smiling, for I have finally found someone I think is worthy to lead the swarm.

POV: Screaming Eagle
Forty-Eight hours later...
I was in command center of one of the defensive positions we established in the lands we took from Equestria when a sentry spotted the distinctive flash of a teleport in the distance. I immediately raised the alarm, only for another sentry to report that she spotted a white flag being waved.

"Get me some soldiers! I want to see who it is!" I ordered as I grabbed my rifle and body armor and rushed out the door.

As I moved to the base entrance, I noticed that nearly every soldier in that base was rushing to see who surrendered, blocking the way for me and obstructing my view at the same time.

"Sweet solar eclipse..." I was stunned when I saw who was at the gate, Princess Twilight Sparkle of Equestria and one of the Zerg creatures our soldiers had encountered. "Open the gate! Let them in!"

"Why would a Zerg worker and Equestrian Princess seek to give up?" I thought to myself as I ran to meet the newcomers.

"Thank you for letting us in." The Element of Magic said as I arrived. "I didn't know where to go, so I went to the one place that might still be safe."

"What do you mean?" I asked her as we went back to the command center. As we walked, I used this opportunity to look her over.

She looked terrible, her mane and tail were unkept, she looked like she hadn't eaten anything or slept in a long time, and I could... feel that something was different with her.

"The Zerg of the Phantom Brood have taken control of Equestria." She answered as we entered the command center. As soon as the door closed I had some food and drinks brought in for the Princess. "Thanks."

"No problem, if it wasn't for this damn war, I would've visited Ponyville and tried to become friends with you." I replied, trying to lighten the mood. "What do you mean by 'taken control'?"

"Simon has implanted some kind of parasite in the other Princesses, turning them into his slaves." I was glad I was drinking anything when she said that or else I would have spat it all over her.

"What?! How did that happen?!" I asked, before realizing something. "How do I know that you've not been infected with one of these parasites? You do have a Zerg companion after all!"

"I was the one who warned Twilight of the infestation." The drone said in what could only be described as a defensive tone. "Also, why would I put my new master under the thrall of the enemy?"

"So you're now one of hers? But our intel said that you zerg have a hivemind, one that all zerg creatures require for higher brain functions." I knew that informing Princess Twilight about our spies in Equestria was risky, but I needed to make sure that this base wasn't in danger.

"I'm special in that regard, for Simon reengineered me to be capable of independent thought." The drone answered before Twilight finished her meal and spoke up.

"I'm willing to join you in the fight against Simon and his Zerg if you provide us with some things." She said as she wiped her mouth. "If fighting the Phantom Brood means that I will have to hurt my fellow ponies, I'm willing to do it as long as it leads to the defeat of Simon."

"What do you need?" I then asked the Princess, only to find out that she fell asleep.

"We'll need a large open space, a steady supply of essence, and for your soldiers to protect us for some time." The drone answered as I had the Princess brought to my quarters so she could rest.

"The first and last ones, we can do easily, but what do you mean by essence?" I asked the crab-like creature before me

"Minerals, Vespene Gas, and dead creatures all provide varying levels of essence." The drone then informed me of the nature of Zerg and their need for essence. "The first two can be found in crystal fields and gas geysers, respectively, while the last one is self-explanatory."

"I'll see what we can do." I said before I went out to collect what we needed and more, for if we are all to survive the Zerg, we're going to need all the help we can get...

Author's Note

Here's the potential for a good ending, Twilight going a similar path to Sarah Kerrigan during the StarCraft 2: Heart of the Swarm campaign!