ALONE AND ON THE RUN

STORY BY Summerset banjo
EDITED BY EppogirlXD & Aktress

Under the cold night sky of the Everfree Forest, a lone, exhausted unicorn sits down next to a tree trunk, and using her horn, she emits a small amount of light allowing her to see the saddlepack she brought with her. Opening it up she sets a small, audio cassette recorder, on the tree trunk and reaching out with her bandaged foreleg, she pushes a button to turn it on.

"My name is Twilight Sparkle. I don't know who's going to listen to this. I don't even know if I'm going to be alive in the next few hours. But I've got to tell the world the truth about what's happened in the last few days. I'm not sure when I noticed that things began going wrong, but I think it was the day after the party. It has been nearly three weeks since we returned from the Crystal Empire. Pinkie Pie thought that celebrations should be in order for finding the Crystal Heart and stopping Sombra. At the party I had a little too much apple cider, so I left the party early and crashed at Rarity's home for the night…"

"…It was around five in the morning when I got up."

Twilight Sparkle woke up in Rarity's spare bedroom, and looking at the alarm clock, she saw it was 5:30 am. "Did I have to wake up this early?" she groaned.
Hearing some noise in the kitchen she got up and entered the kitchen. There at the table was Rarity having breakfast.

"What are you doing up so early?" asked Twilight while pouring cereal for herself.

Briefly glancing up at Twilight, Rarity responded, "I have a lot of work today. Thought I should get an early start."

"At five thirty in the morning?" said Twilight in surprise while pouring milk into the cereal.

"I have several dresses that need to be designed, made, and shipped out of here before sundown."
Rarity's cat crept into the room. Twilight looked over to the cat and smiled. "Good morning, Opal. How are you this morning?" She reached over to pet the small cat but Opal hissed and tried to scratch at her before running off.

She looked at Rarity with surprise. "What did I do to deserve that?"

Rarity just scowled and said. "It's just a phase, Twilight. She doesn't mean it."

"Huh?"

"Don't let it bother you." Rarity got up to put her dishes away in the sink.
Twilight was nearly finished with breakfast when she asked another question. "What time did you leave the party?"

Rarity went over to a small work table near the kitchen and started doing some sketch work on some papers. "I don't know. Late. I didn't want to wake you."

Twilight got up and put the cereal bowl in the sink, then used her horn to open a cabinet to put the cereal box away. "I was tired. I guess going to a party after returning from Canterlot took a lot more out of me than I thought."

Rarity stopped working on the sketches and looked up at Twilight with sudden interest. "What did they have you do up there?"
"In Canterlot? Well mostly they had me look over the new security measures the guards there had put in place for the negotiations, as we don't want Cadance's return be as eventful as her wedding. I wish my brother was there yesterday. He would have had a field day."

Rarity suddenly got up and started gathering her sketch papers. "I need to get going, to gather the materials I need."
"Since you're busy, don't worry about taking Sweetie Belle to school, I'll take her when it's time," said Twilight.

Rarity walked over to the base of the stairs. "Don't bother; I'm taking her with me. Sweetie Belle!"

"To school? When you're rushing around getting dress material? That doesn't make sense." Twilight asked, confused over Rarity's strange behavior.

"Cheerilee wants to talk to me and Sweetie Belle about her falling grades."

"Rarity it's only now six o'clock! Teachers don't talk to students this early."

Rarity just shrugged. "I guess Cheerilee wanted to do it while her mind was still fresh."

"If you say so…" Twilight started heading towards the front door. "I guess I'll head back to my home now."

"See you later... Sweetie Belle, come on!"

On her way back to the library, Twilight spotted a couple of guards from Canterlot looking around and talking to one another. She approached the two. "May I help you two?"

The guard on the right spoke up. "We're just finding spots to construct security checkpoints."

The guard on the left then spoke up. "We need to be ready if any problems come up when Cadance visits this town, after the talks in Canterlot are finished, Miss Sparkle."

"But I thought the plan was to wait, until my brother arrives to look over the security for the summit, before we start to implement it," Twilight said, surprised.

The guard on the right spoke up again. "The Commander didn't feel that we should wait for Shining Armor."
"But that's not the plan that everypony agreed upon yesterday. Why is Commander Tri-Star changing the security arrangements?" Twilight said with growing frustration.

The guard on the left stared at Twilight for a moment before speaking. "We're only following orders. You will have to talk to the Commander about the change in plans; he's currently at the town square."

"I most certainly will," muttered Twilight walking past the two guards.
Quickly, Twilight arrived at the town square and spotted Tri-Star walking towards the town hall. She started to approach him, but stopped in her tracks when witnessing the strange sight before her. Rarity walked out of the town hall and greeted Tri-Star before the both of them went back inside.

"This was when I realized that everyone was acting a little odd, from Rarity's bizarre behavior to Tri-Star's sudden change of plans I just chalked it up to a bad mane day, I mean who could've guessed what was really going on at that point…?"

Snap!

"Huh?! What was that?!" Twilight whispered in a panic before turning off the audio recorder.

Dimming the light from her horn, she listened carefully for any other noise of movement. Seconds passed and no other sound was heard. She cast a spell that detected nearby life. There was nothing but a small animal.

Twilight turned the audio recorder back on. "When I saw that I missed my chance to talk to Tri-Star, I decided to head back to the library, still puzzled on why Rarity was at the town hall talking to Tri-Star instead of getting those dress materials or taking her sister to school. I did not know at that point that I would soon loose Spike…"

"It was at the library around eight when I got the heart-breaking news."

Twilight opened the library door, taking note how it seemed to be cleaner than usual. "Spike, are you here?"

"I'm up here, Twilight," said Spike from the living quarters. Spike sounded upset, and Twilight knew something was wrong.

Twilight climbed up the stairs to the library bedrooms and reaching the top of the stairs she saw the baby dragon packing items away in a small suitcase. "Spike, what are you doing?"

Spike looked up at Twilight with sorrowful eyes. "I'm leaving Twi; I'll probably never see you or this town again."

Twilight walked over to Spike with a worried expression on her face. "What are you talking about?"

Spike sat down on the bed. "I got a letter saying that my services here are no longer needed, and that I have to return to Canterlot, to be reassigned to a new pony."

"What?! Let me see this letter!" Twilight yelled, in complete shock.

Spike reached inside the suitcase and pulled out the letter. "Here it is."

Twilight used her magic to pull the letter out of Spike's grasp and began to study the letter intensely. "I can't believe this." Twilight set the letter down. "It's authentic. Written and signed by the Princess herself," Twilight said with sadness in her voice. She sat down on the bed next to Spike and held him close.

"Twi, please don't tell the others that I'm leaving. It's hard enough to say goodbye to you without… sniff." Tears were starting to form in Spike's eyes.

"I understand," Twilight said softly.

"Twilight… can you walk with me to the train, when I'm finished packing?"

Twilight looked down at Spike. He could see a single tear run down her cheek as she looked at him. "Sure."

Spike got off the bed and went back to packing the suitcase.

"I kept my word and did not tell anypony about Spike's departure until after he was already on the train."

"It's too bad I'll never be able to tell Rarity how much I truly loved her," Spike said looking out the train car window. "Promise you'll keep the library in one piece, Twi?"

Nodding, Twilight gave Spike a hug. "Spike, I promised that I would never get rid of you, and I'm going to keep my word. The next time I have an audience with Celestia, I will talk to her about getting you back with me." She said with determination ringing through her voice. He looked away from the window and shook his head.
"It's not going to make a difference. Celestia herself sent that letter, she's not going change her mind."

"Everypony that doesn't have a ticket needs to leave the train now. We will be leaving in a few moments." the conductor announced.

"Well I guess you need to leave now. Goodbye, Twilight. I'm sure going to miss being with you." Spike said to Twilight and hugged her one last time before Twilight left Spike's side and trotted out of the train. She got off the train stopping for a moment to wipe a tear away from her cheek.

She stood on the station platform watching as other ponies got off the train. Looking down the length of the train She saw something odd going on at one of the freight cars. Further down the platform stood Rarity and Applejack, busy loading some unmarked crates on to one of the train's freight cars. Twilight walked towards the two but stopped when Pinkie Pie appeared in her path.
"Hiya Twilight! Why were you helping Spike onto the train?"

Twilight looked over past Pinkie Pie and saw that Applejack and Rarity were eyeing both of them suspiciously before going back to loading the unmarked crates. "Spike's leaving us for good. Pinkie, he's being transferred to work with a new pony."

"Well that's silly. Why didn't Spike tell anyone that he was leaving. I could've given him a farewell par-"

"He didn't want anyone to know, Pinkie!" Twilight said sharply before letting out a frustrated sigh. "Sorry… It's just that Spike's been with me for so long. It's hard to see him go."

Pinkie Pie looked at Twilight for a moment before saying, "Come by the Sugar Cube tomorrow night, I'll fix you dinner. It will make you feel better."

"All aboard!" the conductor yelled, before the train started rolling down the tracks. "Thanks Pinkie, I'll take you up on that."

"Oh goodie." Pinkie ran off in excitement and when Twilight looked at where Rarity and Applejack were at they were gone.

"I stayed at the train station for a while, watching the train slowly roll down the tracks until it was far off in the distance. It was sadly the last I saw of Spike, I eventually left to go back home when I ran into to Commander Tri-Star."

"I was told you wanted to speak with me, Miss Twilight, and from what I heard you were a little upset," said the unicorn guard.

"Yes, I am," replied Twilight.

"Well you have every right to be, Miss Twilight. I'm sorry, but I decided to accelerate security preparations here, as I felt that this town was less secure than Canterlot and it would be better to have everything in place before your brother looked it over instead of after. I guess I forgot to inform you of the change of plans." He smiled apologetically.

"Yes, well I like to stay in the loop."

"It's getting late, I'll walk you back to your house," offered Tri-Star.

"Sure." Twilight nodded in agreement.

"I've read over your report on the Crystal Empire delegates again. They seem to be quite concerned with security."

"They're probably just little paranoid, it's been 1,000 years since they left the empire and visited another land. So it's a bit intimidating for them to acclimated to modern society.

"Is there anything else I should know about them?"

"No. But you were there at the security meeting yesterday, so you should know all about them."

"I'm talking about stuff not put in reports."

"What do mean?"

"You know, the kind of things we don't include in reports but might be useful for security."

"I'd have to give it some thought…" She paused for a moment before continuing. "I…guess…there's one thing you should know, Princess Cadance used to be my foal sitter, and since I was the one that helped get her out of the caves she probably trusts me over most ponies."

"Hmm… That might be helpful to know," Tri-Star said deep in thought before continuing. "Tomorrow everypony in Ponyville will be undergoing a medical examination. Before I leave tomorrow I need you to do a job for me."

"What kind of job?"

"Well, your report on Changelings has disappeared earlier today, so I need you to send me another copy before I leave."

"Tri-Star, that thirty page report was the only copy I made. How did you lose it?

"Can you write the paper again?" asked Tri-Star, ignoring her question.

"I can, but it's going take a while. Are you sure you can't find it?"

"Positive. You can hand me this report around one in the afternoon tomorrow I…argh!" Tri-Star stumbled with pain for a moment holding a hoof to his forehead.

"What's wrong?" Twilight said with concern.

Tri-Star gave a reassuring smile to Twilight. "Nothing, it's just a headache, been getting them on and off all day, probably due to stress…what I was going to tell you? Oh well, maybe it will come to me later… That's your house up ahead. I need to return to the town hall now." Tri-Star turned to leave.

"Wait, one last thing before you go. I saw you talking to one of my friends today. Her name is Rarity. May I ask what she wanted to talk to you about?"

He stood there for a moment before saying, "I'm sorry but that name doesn't ring a bell. Oh well, good day Miss Twilight."

"Tri-Star was telling the truth about one thing at least: the Changeling report was indeed missing. I quickly set to work on making a new paper based on my notes. As I wrote I couldn't help but think that this was going to keep me busy for the rest of the day. When I finally finished it in the early hours of the morning I realized how quiet and lonely the library felt without Spike being there. The next day I went to the hospital to get examined."

"I've been here for over two hours now. Are all the tests on me done?" asked Twilight with an annoyed tone.

"All that's left is a blood sample and then you'll be done," responded the Nurse setting out a small tray containing the syringe and several empty vials.

"Good. I have to send in a report to Tri-Star as soon as I can leave here." Twilight said feeling a bit relived from the news.

"Ok, stick your right foreleg forward," said the Nurse while preparing the syringe.

Twilight looked at the nurse and noticed a look of worry on the Nurse's face. "Is there something wrong? Is it my health?"
The nurse prepped part of the leg for the blood test. "You so far have a clean bill of health…" The nurse poked Twilights leg with the syringe and started to withdraw blood from it. Twilight only mildly grunted at the slight pain of it. "…What's really bothering me is that yesterday afternoon some of our medical supplies were stolen. Nopony has seen anyone taking the supplies. It just simply vanished without a trace."

"What supplies were taken?" Twilight asked with curiosity.

"Well as far as I know they took several tranquilizers, a field medical bag, and a few other items," said the nurse removing the needle and applying a bandage. "All right we're all done. You can take that bandage off in a couple of hours."

"Thanks, Nurse." Twilight left the room and went into the lobby, which was filled to capacity with ponies from the youngest to the oldest. Almost everyone in Ponyville seemed to be in the lobby waiting to get examined, and after working her way through the crowd she made it outside.

"Hi, Twilight!" said somepony behind her. Turning around she saw it was Rarity's little sister Sweetie Belle.

"Hello, Sweetie Belle." Greeted Twilight.

"May I talk to you?" Sweetie Belle asked politely.

"Uh… Sure but you'll have to follow me. I'm in a hurry." Twilight started walking towards the town hall with Sweetie Belle following close behind.

"Twilight, I would like to have you teach me magic." Sweetie Belle said looking hopefully at Twilight.

"Really? Isn't your sister already teaching you how to use your horn?"

"Yes, but most of her knowledge is based around dressmaking, I want a broader range of skills if it will help me get my cutie mark."

"Learning magic is not as easy as it sounds. It takes time and effort to learn even some of the most basic of spells. Are you sure?" asked Twilight. She wanted to be certain that this is what the little foal wanted to do.

"Yes, I'm sure." Sweetie Belle said with resounding confidence.

"Okay I'll have to talk to your sister first, before I take you on as an apprentice. Besides it's a chance to be able help you with your failing grades." Twilight said with a smile.

The young filly looked at Twilight, confused. "But my grades are fine Twi. In fact I was given an A plus yesterday."

"It was at this moment when I realized that there was something definitely suspicious going on with Rarity, so I decided to find out what I could from Sweetie Belle."

"On second thought, how about you have dinner with me tonight at the Sugar Cube Corner. We can discuss your internship there."

"Oh that would be great!" Sweetie Belle was almost giddy with excitement.

Twilight looked around to see if anyone was watching before leaning close to the small foal. "Sweetie Belle, did anything unusual happen when I was gone at that meeting in Canterlot?"

"Sweetie Belle!" A blue blur swooped down in front of the two. It was the pegasus, Rainbow Dash.

"I'm glad I found you. Rarity's been looking for you. She's back at her house now waiting to talk to you. It seems to be important."

"See you later." Sweetie Belle ran off towards Rarity's house.

"Hey Rainbow Dash can I talk to you for a…"

"Can't. Gotta go bye." Dash said abruptly before flying off.

Twilight just sighed with disappointment before reaching the town hall. In front of the town hall stood a royal guard. Twilight approached him. "Excuse me, but may I speak to Commander Tri-Star?"

"I'm sorry, but he's not here."

"What?"

"He left for Canterlot last night."

"But he told me to meet him here today! Uggh." Twilight grunted with disgust. "Fine! I will send it to him by mail." Twilight marched off to the post office.

"It took me the better part of the day to get the package delivered, from long lines to trying to get the report to fit inside the package. It definitely made me wish I still had an assistant. When I was done I saw it was time for dinner with Pinkie Pie. It was at the Sugar Cube Corner, when I started to learn of the threat that Equestria now faces."

Twilight arrived at Sugar Cube Corner she noticed that the store was closed. She knocked on the door of the pastry shop. After waiting for a moment, she knocked again. "Come on Pinkie, open the door." Twilight muttered under her breath.

The door slowly opened with Pinkie Pie standing just inside the shop. "I'm glad you made it Twilight! Come on in."

When Twilight entered she noticed the lights inside were dimmed giving the normally cheery shop a somewhat moody atmosphere.

"Hey Pinkie, why is the shop closed?" Twilight asked as Pinkie shut the door.

"I didn't want anypony to bother us when have our dinner. It's just a party of two after all." Twilight was surprised by Pinkie Pie's strangely serious tone of voice and attitude.

Clearing her throat she started to speak. "Um…Pinkie I invited Sweetie Belle over to have dinner with us so we may want to wait…"

"Don't worry about Sweetie Belle, Twilight. Rarity came by a few minutes ago telling me that she can't make it tonight. She isn't feeling well."

"Strange. She seemed fine a few hours ago." Twilight said following Pinkie Pie to the table. She suddenly realized the Cakes where nowhere in the shop. "Where are the Cakes?" she asked as she sat down at the table.

"They're…." Pinkie started to grin. "…in the basement playing with the babies, they didn't want to bother the party," she said still grinning. Her grin seemed somewhat off. The way she was smiling was starting to make Twilight feel uncomfortable.

Ding! Something chimed in the kitchen. "I'll be right back." Pinkie Pie walked out of the room and into the kitchen.

As soon as she was gone Twilight got up and walked over to the flight of stairs that lead to the basement. Looking down she saw that it was pitch black down there and completely silent. Twilight started to feel quite nervous and she quickly hurried back to the table and sat down just in time for Pinkie to return with a single plate. She sat it down on the table in front of Twilight Pinkie then pulled up a chair and sat across from Twilight.

"Twilight, I understand how you feel losing a friend. I lost several friends myself when I moved here. Life's a party Twilight, but a party's no fun without friends." Pinkie Pie got up again and stepped into the kitchen briefly before returning with a tray full of cupcakes, setting them down on the table.

Twilight noticed there was only one plate on the table. "You forgot to set out a plate for yourself." Twilight said with a nervous grin.

"Not hungry." Pinkie said sitting back down across the table.

"Not…hungry?" Twilight said with disbelief.

"Yep. Had a late lunch." Pinkie Pie reached over picking up a cupcake and placed it on Twilight's plate.

"Here you go Twilight." She gave a broad smile.

Twilight was starting to sweat as she looked down at the cupcake before her. Nervously she looked back up and saw that Pinkie Pie was still sitting there staring at her. Twilight looked at the cupcake again, before bringing the plate closer to herself. She looked at Pinkie who was grinning even wider than before, clearly watching her every movement. Twilight's hoof was starting to shake as she started move it closer to the cupcake.

"How is it?" Pinkie asked, licking her lips with anticipation.

Twilight picked up the cupcake and stared at it for a moment before putting it back on the plate. "I think I should go home and lay down." Twilight got up from the table.

Pinkie's smile turned into a scowl. "You haven't eaten a bite," she said with growing anger in her voice.

Twilight gulped and tried to calm the angry mare. "I just don't seem to have an appetite right now."

Pinkie just sat there at the table glaring at Twilight as she walked out of the Sugar Cube Corner.

"I don't know if there was anything wrong with the cupcake or not. But all I could think of, as I looked at her, was that this was not Pinkie Pie…"

Twilight started coughing for a full minute before regaining composure. "I'm sorry. Where was I…? Oh yes. I did not get much sleep that night. The next day I started my search. I had no idea what I was looking for. Something odd, something not quite normal, anything to explain what might be going on."

Twilight finished putting the last spell book back on the shelf and wiped the sweat off her brow before picking up the checklist she made earlier that morning. "It's not chemical agents, there's not any unusual magic at work, no telepathic activity that I can tell, and it's not anything transdimensional ether." Twilight rubbed her forehead with frustration. "This only leaves a few possibilities left, but I need to have more information to be sure."

Twilight hid the checklist under one of the floorboards and left the library.

"I needed to look at the town records and while they're normally available for the public, the types of records I needed to see, required special permission from the mayor herself."
Twilight approached the guard at the front door of the town hall. "State your order of business." the guard said gruffly.

"I need to speak to the mayor."

The guard shook his head. "Sorry. No one is allowed into the town hall without special clearance."

"Here. It's a level 1 security pass." Twilight handed the guard her pass card.

The guard looked at the card then at her. "Sorry. The card doesn't have the proper numbers needed to be allowed inside." The guard handed Twilight her card back.

"But I'm Celestia's student and the one of the bearer's of the elements of harmony. Surely you could let me see the mayor!" insisted Twilight.

"Sorry, but I've got my orders. No clearance, no access."

"I will be back soon with proper ID." Twilight grumbled as she left town hall and trotted to the guard house. On the way there Twilight started to feel sick to stomach and then a little woozy which forced her to sit at bench for a moment before it passed.

"At first I thought it might have been a delayed reaction to the blood test. But now I'm not sure."

Twilight entered the guard house and approached the mare at the front desk. "I need to get security clearance for the town hall please."

The guardsmare looked at the card Twilight handed her. Then she tore the card in two.

"Why did you do that?" Twilight said, shocked.

"Your name has been removed from the security detail in charge of the summit."

"On who's authority?!" growled Twilight.

"Why...Commander Tri-Star, of course."

Twilight's anger subsided when she realized who sent the order. Then it dawned on her. "The missing report… the headaches…denying the meeting with Rarity…it couldn't be could it?" she muttered under her breath.

"Are you okay? You look a little sick." The guard behind the desk said with concern.

"No…I'm fine. Thanks for informing me." Twilight left the guard house hurrying back home.

"It was as I feared. It appeared that the Changelings may have returned to Equestria. Celestia said to trust my instincts if I sensed something wrong. But I wanted to be certain, so that night I broke into the town records office. There were a few traps in place to alert guards of a break in, but they were easy to avoid. I started as far back as the day of the wedding, since that was the first known appearance of them. It took several hours going over all sorts of records and reports, and then when I finally got to the day I left for the security meeting, I discovered something shocking. All pages after the date I left were completely blank! Security reports, train manifests, mail shipments…It didn't matter what records I looked in, there was not a single entry.

I nearly gave up looking when I peered into the office trash bin. What I found in the trash bin did not answer everything but it did confirm my suspicions. With the badly burnt report I found, they have been analyzing and reanalyzing what I know about Cadance and the other delegates. There were also several mentions of receiving some messages from Canterlot but sadly that part was too charred to learn the details of the messages. I took the paper out of the trash bin and brought it with me back to my house.
When I made it back to my house I found it in state of disarray. Someone had broken into the library and ransacked the place while I was gone. If I had stayed at home that night they would probably have nabbed me. I stayed up for the rest of the night on guard in case they returned."

"We have yet to search this part of the woods!" a voice shouted in the distance.

Twilight's ear perked at the noise and she quickly dimmed her horn light and again cast the life detecting spell. "There appears to be three ponies probably guards," she whispered to herself before turning off the recorder and putting it back in the pack. "I need to hide somewhere…"