Author's Note

FYI: This story partially follows the premise of "The Matrix".

Regret

Twilight Sparkle and Flurry Heart had escaped the machines' clutches and found where Neighsay had set up a base in the wilderness along with a handful of other citizens from Equestria at an early point in the war. The sky was no longer sunny, as the machines were once dependent on solar power. To counteract this, Flurry Heart had cast a spell to block the sunlight by wrapping dark storm clouds around the globe. Starlight Glimmer was the only one of Twilight's friends that had evaded capture in the beginning. Her other friends had been captured by the machines. Starlight's location was unknown, so it was assumed that the machines had captured her at this point.

Neighsay had been having a mental breakdown since the beginning of the war. It was his own dream to create an automated system that would assist with keeping track of records and archives of recent events. 20 years ago, the AI had started creating its own mechanical beings and arming them with weapons. When the robots began attacking Equestria, Neighsay came to realize that his own creation had turned against him. He soon returned to his senses and later called a meeting With Twilight and her niece. When they arrived in his office, they immediately saw that he was wearing a badge that signified him as the Commander.

"I regret creating Artificial Intelligence at such an early time. I was not aware that my own creation would betray me and start a war against us," Neighsay said to Twilight and Flurry.

"It isn't your fault. You didn't know this would happen. Aunt Twilight and I are lucky we managed to break out of the "Realm" that the machines created," Flurry replied.

"She's right, Neighsay. If we had been in there for any longer, we'd probably have been killed trying to get away," Twilight added.

"What is this "Realm" you are talking about?", Neighsay asked out of confusion.

"The "Realm" is a computer generated reality where strict order is kept by the machines. We do not know how we were taken out. All we remember is we suddenly felt dizzy and we collapsed in agonizing pain. When we woke up, we were in fluid-filled pods with breathing tubes down our throats. We sat up and broke through the membranous layer over the pods and saw that we were in a gigantic cave among thousands of other captives. As we pulled the breathing tubes out, we felt as if something was pulling on us and discovered that cables were connected to halos that contacted these spots around our heads. There was also a cable that connected to a port that ran to our heart. The cables started breaking off of us and we were pulled down tubes by the current that the fluid created as it flowed out of the pods. We splashed into a pool and began swimming toward ladders. I cast a spell to block the sunlight and hopefully stop the machines. As we started making our way to find shelter, we came across Starlight who told us about the "Realm" and that the machines were capturing citizens from around the world and killing others. She led us to where she had set up a hacking point to rescue us from the "Realm". She gave us some of the equipment that she had stolen from the machines for us to bring here.", Flurry explained.

"She also told us that the captured citizens were being used as a secondary power source in case the sun was blocked. Now, the machines run completely on bioelectricity. She led us to another cave where smaller pods were held on tree-like structures. We managed to sneak through and discovered that the machines are spawning new captives by using bioengineering."

Neighsay was disgusted by the testimony. He could not believe that his creation had done all of this. However, there was one more thing he didn't understand. When Twilight and Flurry walked into his office, he noticed swollen purple spots on their front legs. He asked what those were. He was in for a nasty surprise.

"According to Starlight, the machines administer nutrients through intravenous lines to keep the captives alive in the real world.", Twilight stated.

"How can they do that? Without the sun, all of the vegetation is dead."

"Good question, you may want to have a bag ready because the process might make you throw up. The machines liquify the dead and pump extracted nutrients through the IV lines. It doesn't matter if they use the captives that have died or if they have dug up the dead from cemeteries, they use it all.", Flurry explained.

As soon as he heard that the machines were liquifying the dead, Neighsay heaved and threw up. Once he had recovered, he spoke again.

"That is downright nasty. I can't believe that this is going on."

Twilight indicated that she and Flurry had found a damaged aircraft and repaired it so they could travel faster. They led Neighsay to where they had landed it in the base and had him get on so he could see what they had told him. It had two seats in the cockpit and two bench seats in the back. At the top were two rings with giant rotors that would tilt for steering. This vehicle was also equipped with guns for defense and they had recently been reloaded. As Twilight started up the rotors and Flurry contacted the gate command post that they were leaving, Neighsay got himself situated and put on his breathing mask because the atmosphere outside the base had recently become unhealthy. Once the gates began to open, Flurry disengaged the landing magnets and they took off. As they flew across the ravaged land, Neighsay saw those that were still fighting the machines. The Equestrians were holding strong, but the machines were forcing them back. Twilight flicked a switch to drop a bomb into the middle of the machine army. The bomb was cloaked from the machines, but the Equestrians saw it coming. It fell to the ground and exploded, taking out 90 percent of the machines, which allowed the Equestrians to charge forth and conquer more ground.

Meanwhile, Twilight continued to fly their gunship over the machines' base and landed in a shielded area where they would not be seen. They trekked into the cave where the captives were being grown for implantation to the Realm. Neighsay gagged when he saw how many there were. The cave stretched downward for miles. Flurry led the way along a path that took them to where she and Twilight were held. He saw bolts of electricity travelling upward as energy was pulled from the captives to power the equipment for the machines. Twilight motioned him to follow her to where the nutrients were harvested. He saw a continuous overhead conveyor moving buckets filled with corpses toward a huge tank filled with a dissolving fluid. He watched in muted horror as one bucket tipped and dumped three corpses into the tank. Numerous pumps ran the nutrient fluid from the tank to the IV lines that fed the captives.

"PSSST, come here.", they heard someone whisper.

They saw a masked pony in the shadows and followed it into a hidden room. The pony took off her mask. It was Starlight. She was not captured. She showed them a crate filled with more equipment that she had stolen from the machines.

"I will follow you back to your base. This equipment will help us rescue more of the captives and help us win this war."

Determined, Neighsay shook hooves with her and she loaded the crate onto a jet she had built from other pieces she had taken. She took off once she saw the gunship and followed them. On the gunship, Twilight had Neighsay put on a headset to inform the ground troops that equipment was being gathered to rescue the captives and help end the war. The troops cheered when they saw Starlight's jet carrying the equipment in the direction of the base. Soon, Starlight had landed and workers were unloading her cargo to create an apparatus for hacking into the Realm on a larger scale.