Disaster Across Equestria

by Snaperkids

Rating: everyone
Tags: Alternate Universe, Human, Main 6, Original Character, My Little Pony: Friendship is Magic, Dark, Cutie Mark Crusaders, Other
Length: 3822

Based on September by TheLivingTombstone Follows an original character through Ponyville

When a biological weapon is detonated near Ponyville, squads of specialized soldiers from all over the galaxy are sent to aid in disaster recovery. Among these is James McCaffrey, a Galactic Council Spectre and lead officer of the United Galactic Fleet. However something seems wrong yet strangely familiar. Can James discover his queer connection and understand the fractured and blurry memories of his dreams?

Published 2012-09-05 13:04:01 UTC
Last updated 2012-12-29 05:01:55 UTC

Response

"Alpha Leader, this is Surface Command; you're cleared to proceed into sector 9 zone 1. Yellow zone support and assessment teams have been dispatched. Over."

"Roger that Surface Command, Alpha Squad proceeding into sector 9 zone 1. Out. Ok, we're cleared to move to the next sector."

"Damn James, I heard this was bad, but I never thought it would be this bad."

"I know Mark, but it's still better than when we had to fight the Ragnar Virus on Pernadow.

"Don't remind me James."

Fleet Admiral James McCaffrey and his squad of 17 was one of 20 squads dispatched to enact a quarantine after a massive spike of FBA's (Foreign Biological Agents). James remembered clearly the events leading up to now. He remembers the patrol, his fighters sensors picking up the spike, enacting protocol 538-E (which states the express need to intervene in planetary affairs of a planet that is a possession and not a council member without pre-approval from council), preparing and briefing quarantine and ground force squads, briefing medical cruisers on their roles in the operation, meeting with Princess Celestia and her sister Princess Luna to get support and intel for the operation, forming fly-by's and airfields for fighters, and the entire operation up to this point. However looking back there's about an hour of time he can't account for.

"Ok James, how do we want to start clearing this area?” Mark asked.

"I'd say we start clearing buildings out. My bio-scanner doesn't register anything out in the open but can't read through the walls of the buildings," Emma said. Emma was one of the three mares in the squad, but was appointed leader of team Charlie (more because no one wanted the position than they wanted her in the position).

"Mark, I think you're losing your edge. Nonetheless the rookie pegged it. Mark, you take your team and clear out that building. Emma, you take that one. My team stay on my six," James pointed out each building as he assigned them. Within seconds the squad had dispersed to begin clearing their assigned locations.

After hours of procedurally clearing out building upon building they came upon what looked to be a giant tree right in the middle of the town. "What the hay is a tree doing here in the middle of a town like this?"

"I have no idea Mark. Why does your hometown have a giant hole at its center?"

"Because Emma, we started out as a mining colony."

"Can you two stop bickering for five seconds!"

"Sorry James," they both said in unison.

"Anyways if you two hadn't started fighting you would have noticed that this 'tree' seems to have a door and windows. I also did scans while you two were arguing and there appears to be life signs."

"So what do we do?" Mark inquired.

"Simple, we change priorities. Emma, your team needs to set up a sterile perimeter. Mark, your team needs to provide tactical support while they set up the perimeter. My team and I will get to work on getting this door open and getting any survivors out. Got it?"

"Got it," and with that Emma and Mark got to work with their assigned roles. James started to pick the lock when a voice started speaking in the back of his mind.

"Who are you and what do you want?" along with this he could feel a presence. Assign of telepathic communication.

"I'm Spectre 519 of the Galactic High Council, Advisor of War and military affairs, Fleet Admiral James McCaffrey. I have been sent to help in the recovery and management of this biological incident. Could you please state your name, rank, and status?"

"My name is Twilight Sparkle. I am the personal student of Princess Celestia and bearer of the Element of Magic. We are currently barricaded in here with limited food and emergency supplies."

"How many are with you and do any of you need any medical assistance?"

"There are 9 of us. We have one who is badly in need of medical care. She has a broken wing and multiple gashes."

"Hold tight. We're working on making it safe for us to enter."

“Perimeter is up you're clear to open the door," Emma stated over the com channel.

At that James filled them in on the information he had gathered from Twilight, and called for a regroup. "Mark, I need you to take everypony who is weapons specialized and form a perimeter. Emma, you're with me. If you have medical certifications you're with me. Now let's go!"

With the speed of a well-seasoned veteran, James had picked the door's lock within seconds. Upon entering James and his team got to work doing bio scans for any signs of infection and attending to the wounds of the injured light blue pegasus with a rainbow mane. The whole thing was completed in a matter of minutes.

"That should do it. Okay James, we're good to go. She should be fine if we can get her back into the green zone," Emma reported having just finished bandaging the last of the gashes.

"Okay I've reported all of this back to Surface Command. They know to expect 8 ponies and one baby dragon."

"Wait, what about Fluttershy? Have you seen her!? Is she okay!?" came a frantic worried voice from behind James. James turned to look at the speaker, a bright pink pony with a pink mane somewhere between curly and frizzy.

"Calm down and tell me who you are first? Now, I don't know of a Fluttershy. Do you know where she is?" James asked trying to calm her down.

"Okay, my name's Pinkie Pie and last I knew she was at her cottage on the edge of the Everfree Forest. Oh, I hope she's okay," Pinkie said after taking several deep breathes.

"Okay, the Everfree Forest is outside of our assigned area, but I can ask the squad leader assigned to that area and see if he came across her. Can you describe her for me?"

"Well she's a yellow pegasus with a pink mane. She loves animals and is extremely shy. Does that help?"

"It's exactly what I need. Now, just give me a second. Alpha Leader to Bravo Leader do you copy?"

"Ahm here, wadda ya want?" came the all too familiar South Gandaro accent (exactly like a Southern American accent) over the radio.

"Hay George, I just needed to ask you if you came across a yellow pegasus with a pink mane out by the forest."

"Well, ah thank ah remember cummin across a pony that looked jus lahk that. Did shay live in a cottage with a helluva lot of critters?"

"Yep, that's probably her what did you do? Where is she now?"

"Ah sent her and her critters back to the green zone."

"Okay, thanks George."

"Mah pleasure."

With that James ended his transmission to the other squad leader and turned to address everypony in the room.

"Well?" a very anxious Pinkie Pie asked concerned for her friends’ safety.

"Good news. They came across her cottage and she's now safe within the green zone," James responded with a very joyous look on his face. This news was taken exceptionally by everypony. "I wouldn't celebrate just yet though," James said making everypony fall silent. "We still need to get back to the green zone." Just as he said this an alarm sounded. "Our shifts over we need to start heading back before it gets too late," he said while silencing the alarm.

The next half hour was filled with getting everypony ready to move to the green zone, a long and tedious process of putting on quarantine suits and connecting air replenishers and reserve air supplies and checking the air sources and getting escorts assigned before finally being ready to head out.

"Mark, you there?"

"Yeah what do you want?"

"We're all set to head back here. Can you do a security scan and start shutting down the sterilizers?"

"Sure thing, I'll get my stallions on it right now."

"Contact me when you're done." For the next five minutes there was complete silence on the radio as Mark and his team powered down the perimeter and scanned the area for any creature that posed a threat to the squad's retreat.

"You're clear," came the team leader's voice over the com channels.

"Okay. Let's head for home." The squad's first priority upon reuniting was getting their bearings. However through the use of the NRT (Navigational Radio Transmitter) network James quickly located there location and got a heading.

The return was for the most part uneventful as the squad encountered very little resistance and was soon back in the green zone. "Okay, Emma can you and Mark escort them to sick bay? I need to fill out the post-op paperwork," James requested with an exhausted sigh.

"Yeah, we'll do that," Emma responded sounding equally tired. However before they could even turn around there came a high, ear-splitting screech.

"Move, we have in coming Scavengers! Get them safe while I cover you!" James barked out knowing the screeches far too well. All around them the sounds of sirens started blaring to alert everypony and get them to battle stations. Soon the sky was illuminated with the bright light of thousands of energy bolts being fired into the sky at the incoming hostiles. Within a minute, fighters were overhead engaging head on into a massive fire fight.

After only a few minutes the sky darkened and the air fell silent. The fighting was over and the Scavengers were on the retreat. James was now ready to collapse.

"Hare's ya paypa' work James," said the documents clerk.

"Thanks Harold, I'll have this back to you by tomorrow morning. See you later," James said as he was leaving.

"See ya round James," Harold replied to his friend.

James had asked around about the yellow pegasus named Fluttershy, and as he suspected she was in one of the barracks with other refugees squads had come across.

Upon entering the barracks he got to work looking for this pink and yellow pony. By asking around he was able to get an approximate location, but even with this there were still quite a few ponies to search through. He noticed many strange and unusual ponies like one that was gray with yellow hair that was wall-eyed, another that had blue hair with blue-green streaks and wore sunglasses, and many others but still couldn't find who he was looking for.

"Spectre 519, this is sick bay, do you copy?"

"I copy you sick bay. What do you want?"

"One of the new arrivals is concerned about her brother and grandmother. I remember sending two refugees to the barracks that match their descriptions can you see I'd you can't find them?"

"Okay, will do just give me a description and names."

"One is an elderly, green mare with gray hair named Granny Smith. The other is a red stallion with sandy brown hair named Big Macintosh."

"Okay, I think I see them I'll contact you once I find them. Spectre 519 out." Sure of his identification he hurried over to speak with the two ponies. "Excuse me, are you Granny Smith and Big Macintosh by any chance?" he asked slightly hesitant of the answer.

"Eeyup," replied the red stallion in a deep, low voice.

"Well, let me introduce myself. My name is James McCaffrey and while on patrol we came across a pony who was asking about her grandmother and brother matching your descriptions."

"That sounds lahk mah sister alright. Where is she?"

"Her and her friends are in sick bay right now going through med checks."

"Excuse me, but did you say her friends are with her?" the voice made James jump for a second even though it was soft. "Oh, I'm sorry I didn't mean to scare you I was just wondering if my friends were okay.” James turned around to face the speaker, a yellow pegasus with a pink mane being comforted by a small, white bunny.

"You're Fluttershy, right? I've been looking for you. A pink pony was asking if you were okay."

"That sounds like Pinkie Pie!" Fluttershy said getting slightly louder from the excitement. "Can I see them?"

"I'm sure they would be happy to see the three of you. If you'll just follow me," he said as he lead the way to sick bay.

As they arrived at sick bay he lead them to where they see doing the medical exams. "I have a surprise!" James called out with an excited tone. Everypony turned to look as he was followed in by the three ponies. The sight of them all being reunited reminded James of his reason for doing this.

"You never cease to amaze me," Mark commented. James just smiled.

Author's Note

I've not yet decided whether or not I'm going to write more chapters. If you want me to write more chapters drop me a comment.

Politics

James looked around at the room he now found himself residing in. It was an empty room, walls either bare or decorated with the signs of deterioration, no windows, a lamp as the room's only source of light, and a single small table with two chairs, of which he took one to wait in. This entire day had been weird and it had only been an hour. After waking up he had gone through his usual routine, first, drop off post-op paperwork and complete today's pre-op forms, afterwards he went to breakfast, past there things got strange. Two officers of a branch he couldn't identify came bearing a summons for his presence. After giving orders to Emma and Mark to get the team to briefing he followed the officers to this room and given orders to wait. That had been about fifteen minutes ago and he had long grown impatient.

Suddenly he heard the door behind him open. Out of pure reflex he reached for his gun expecting a fight. Instead of this however he heard an all too familiar voice. "Ya always were a hothead Lucky. Though I see ya made something out of it, now that you’re Fleet Admiral," the new party quipped. James relaxed with a sigh of relief, for, though it had been years, he knew the owner of that voice.

"Commander Kathleen Renee Shepard, how have you been?" he said ecstatic at seeing his old friend and CO again.” More importantly, what are you doing here, Kathy?"

"I've been doing fine. Though why I'm here is actually a much more complicated question to answer. Take a seat." James knew what that phrase entailed, for he knew she knew him well enough that he hated getting news while sitting down. He opted to remain standing instead.

"What's this about?" he scoffed, irritated at having to be dance around bad news.

"Well as you know the Committee on Planetary Interference was established in order to regulate the interference of the Council on the political functions, economic stability, cultural metamorphoses, and technological development of planet’s inhabitants. You also know that they are also tasked with monitoring the United Galactic Fleets movements."

"Yes. Yes, I know all of that I helped form the committee. What does this have to do with me?"

"I'm getting there, just hold on. If you haven't heard about three months ago I was reinstated as a Spectre after completing a covert assignment, the details of which are still classified. I was assigned to one of the members that deals with a lot of biological research. When we discovered an unauthorized ejection of a biohazard class 12-C containment vessel and tracked it here, we informed the Committee. Their response was to this was to redefine your role in responding to it. They sent me to carry this message."

Shepard hoofed James a sealed envelope. Inside this envelope was a piece of paper with his new objectives and role. It read:

To the position of Head of Quarantine Squad Operations:

Your operations have been reevaluated and, after much consideration, we as a collective feel that your initial objectives risked immense interference upon the natives; therefore your new role is to:

• Destroy any remnants of the pathogen
• Contain the area which the pathogen has already infected
• Recover the pathogens containment vessel

We hope these changes are not too difficult for you to accommodate.

Respectfully,

Ronald K. Pontechnak,

Chairman of the Committee on Planetary Interference

After finishing reading the letter, James took a seat in silence, trapped in thought of how to work around these new restrictions. "These are completely impractical," he finally scoffed. "They don't take into account for the anarchy or the fact that the pathogen was released from its container."

"Unfortunately I already knew that when I was assigned to oversee your operation, but what do you want me? They expect me to send them updates on your progress."

"Report our progress then just neglect to mention what they don't need to know."

"And when they find out about this? What then?"

"Let me take care of that," on this note their meeting adjourned. James left to finish preparing for his squad's mission and within an hour they were out in the field.

Immediately after they had moved out of earshot of the base James was flooded with questions about what the meeting was about. These questions were quickly dispatched quelling everyone’s concerns. "Now let’s get going we have a fairly dense area to clear with a lot of area today," James said leading the way to the sectors they were supposed to clear that day.

That day started out rather uneventful, repeating a routine clear and secure maneuver for urban environments, but after lunch things started to get interesting. It first started with a Scavenger drop ship deploying troops; however things quickly snowballed out of control as infected hosts quickly surfaced and began launching attacks wave after unrelenting wave.

"Fall back, we need a better position," James barked out knowing that there current position was indefensible. They were falling back, still laying down suppressing fire to keep the hordes away, when the most horrid and gut-wrenching sound filled the air. The shriek of pain from a team member.

James turned to see they had been flanked by a group of about five infected ponies. Without a second of hesitation he readied his weapon and fired upon the group which quickly retreated.

"Emma, any luck finding somewhere we can hold up in," James inquired his partner knowing they desperately needed a defensible location to administer first aid and call for support.

"Found one. Thirty meters south-southwest, I’m sending you a waypoint now."

"Let's move." The following minutes felt like hours, the air filled with the sound of suppressive fire as the squad fell back.

Finally out of the fray, the squad could relax. James looked at the time, an hour till they had to return. "Silence push E-5-19, I repeat silence push E-5-19," James called into his radio. "This is field team lead 0-0-2-3 calling for tactical support. We are pinned down by hostiles and need air support for an emergency withdrawal. Do you copy?" James waited for a response to his plea for help; however after several minutes with no response he knew his transmission was not received.

"No response, they must be on radio silence," responded James to Mark's query about the request for support. Minutes had passed with nothing more than white noise in response prompting Mark to call a team leader meeting to figure out a plan of action. "We better start setting up camp. Without any type NW-7 attachments or advanced scans, trying to get back to base would be a suicide mission."

"Okay, let's get started then. We have a long night ahead of us," Emma spouted out in a pseudo enthusiastic tone.

Author's Note

Commander Shepard was used not to infer a crossover with the Mass Effect universe but because it was the only surname that I could think of that sounded nice. It's not a crossover, it's a reference at most. Sorry for the letter formatting the old text in square braces was my formatting when writing. The current formatting is the best I could do.

Dreams

"Finally I'm done," James thought to himself finishing the last of his post-op paperwork (and trust me when I say that is the true test of sanity for squad leaders). He look at the clock.

"1:30 in the morning. Oh how I hate paperwork. Oh well, at least now I can finally go to sleep." He walked over to his bunk and within two minutes of laying down he was dead asleep.

Falling. All he could see was falling.But this was like a different kind of falling. He knew he was falling but he didn't feel wind rushing past him or a weight pushing him downwards. He just knew he was falling. Then, stopping.

"Ah!" The suddenness of the impact jarring him out of his sleep. Alter a few seconds of trying to understand what just happened he noticed something peculiar.

"The room. Everything's missing." He got up and walked around trying to find proof that this was all just a holographic projection. Quickly he realized that this wasn't a projection, and started looking for answers in this white, barren, ezexpanse of nothing.

Suddenly he heard something. Wings? He turned around and right in front of him was a raven staring right back at him.

"Where did you come from?" James asked not expecting a reply.

"I came from you, Saroni," said a deep, booming voice.

"Who said that?" James said completely surprised by the unknown source of the voice."

"I'm right here, Saroni. I believe you refer to my form as that of a raven. Am I wrong?"

"Why are you here?"

"I am here to be you're guide and help you uncover answers to your questions, Saroni."

"Ok, so guide me. Show me what I need to know."

"That I will do, Saroni." Promptly after saying this the raven's eye began to glow. The air around them was filled with the sound of sword fighting.

"James! James, Wake up!" It was Mark, "Come on its 5:30 you need to get ready for briefing. It's not usual for you to sleep in like this."

"Okay, okay I'm going. Sorry I just had a long night last night, James said rushing out to get ready.

Author's Note

Its been awhile since I last posted a chapter, this is kind of a parallel storyline to the main one and this will probably be the shortest chapter of this storyline. Hope that you like it. Chapter three will go back to the main storyline.