NCIS - The Endless Sea

by Mkchief34

Rating: mature
Tags: My Little Pony: Friendship is Magic, Other, Thriller, Mystery, Spike, Violence, Crossover, Human, Main 6, Princess Luna, Drama
Length: 4196

When a Marine Lance Corporal, currently on liaison with the Equestrian Royal Navy, is nearly killed, Gibbs and his team investigate.

NCIS Agent Leroy Jethro Gibbs, accompanied by his team, Dr. Mallard, ME-Assistant Palmer, and Forensic Expert Abby Sciuto, are sent to Equestria in order to assist with a critical case. A US Marine Lance Corporal, who was leading a joint American and Equestrian Navy improvement program, was attacked and left for dead outside the Equestrian Navy’s main shipyard.

With two respective governments behind them, The team sets to work and soon unravels a vast conspiracy that will take them from the South Sea naval yard, to the town of Ponyville, and all the way to the ivory and gold-clad towers of Canterlot. With plenty of known allies and unknown enemies, there’s plenty of work to be done…and Gibbs and his team are just the ones to do it.

Published 2022-06-17 12:40:01 UTC
Last updated 2022-12-05 20:06:50 UTC

Prologue - Blood in the Water

Realm of Equestria, Southsea Royal Naval Yard

10:20 PM

The scent of the sea salt in the air was thick enough that you could season your breakfast with it, thought the pegasus pony Bright Sky, a crewpony in the Equestrian Royal Navy. He and his assigned partner, a unicorn Lieutenant named Steel Blue, were currently on night patrol around the Naval Yard.

Bright Sky had to admit, the evening was quiet enough that he wanted to stay in his bunk, but Steel Blue had chosen to mentor him, so there wasn’t much of a choice to begin with. As a new recruit, each crewpony in the Navy was assigned a mentor of a higher rank to help them accustom to Navy decorum and a new life at sea.

It had only been six months since his enlistment, and yet Admiral Fairwind, the head of the Equestrian Navy, had commended Bright Sky and his class of recruits for their model service so far. As a reward, he and his class had been invited to the officer’s club three nights ago for drinks.

It would’ve been an event to remember on its own, but Bright Sky had overheard the officers and the Admiral talking about some “visiting advisors” that were due to arrive the next evening, and how their “arrangements” were to be seen to by the Lieutenants in charge.

Bright Sky hadn’t thought too much of it, until the next afternoon where every crewpony was ordered to sea for weather-control drills, and only the command staff were to remain at the Yard to oversee those drills.

It had taken five hours before they could return, and right now, Bright Sky was really missing his bunk.

“Sir?” He managed to ask Blue Steel. “May I ask a question?”

“Go ahead.” Blue Steel asked as they stopped at the front gates. “We’ve got about ten minutes before the next rotation.”

“Is there something going on that we’re not supposed to know about?” Sky asked. “I overheard you and the command staff talking about some visiting advisors while we were at the officer’s club. I didn’t really think about it until the weather-control drills, when we had to vacate the Yard. May I ask what’s happening?”

“Well, I suppose I won’t get into too much trouble if I tell you, since the other lieutenants are telling everypony else what’s going on in the morning.” Blue Steel shrugged. “Those visiting advisors are here from another world at the request of Princess Celestia.”

“Before you even ask anything else, let me explain.” He continued, seeing Bright Sky’s dumbfounded expression. “There’s eight of them, they’re called humans, and are all soldiers like us. More specifically, they’re called “Marines”, a kind of naval-based soldier.”

“They’re here to help the Royal Navy develop a marine unit of our own, and instruct us in usage of their technology and equipment. We needed the Yard vacated so we, along with Princess Luna, could meet with them and their leadership.”

“The reason we needed total secrecy was that we’re still negotiating with their nation’s government about a full public reveal, and seeing as their kind doesn’t use magic, it’s a two way street. They learn about us, we learn about them, et cetera.”

“They don’t use magic?” Bright Sky whispered, astonished even more.

“Nope, they prefer technology to magic, and I have to admit, they’re a lot more advanced than we are in that way. I mean, they have a ship class called an aircraft carrier that’s around 1100 feet in length, on average. Our biggest frigate is only 135”

“Sweet Celestia.” Bright Sky cursed, before quickly apologizing for his language. Blue Steel was about to respond when he heard something that startled him. It was a faint cry for help, and judging by the weak volume, it was close.

The two Equestrians immediately sprinted around the corner and out of the main gate, to see a shocking sight. It was one of the human marines, and judging from the bleeding wound in his side and his groans of pain, he had been attacked in a rather brutal fashion.

Blue Steel immediately began screaming for a medic using a voice-amplification spell, and alarm bells soon began to ring across the yard. Steel then ordered Bright Sky to head to the Admiral’s office and tell him of this immediately while Steel performed whatever first aid he could.

As Bright Sky took to the air at breakneck speed, Blue Steel frantically applied a medkit and used healing magic to seal the wound. The marine nodded back weakly, expressing his thanks, before he fell limp.

At that moment, the medics arrived and took over, moving the marine onto a stretcher to move him to the Naval Yard’s medical wing, while also performing more advanced healing magic. In the chaos, Blue Steel picked up a silver object on a chain that lay in a pool of blood, pocketed it to return it later, and moved to follow.

As the light reflected off of the dog tags, the inscription on them could be clearly red.

US MARINES
SIMMONS
DEREK J.
27-35-4456
A-POS
CATHOLIC

====

The Next Morning…

Planet Earth, United States of America, Quantico, VA
NCIS HQ, Main Work Room, 8:30 AM

As the elevator emitted a “Ding!” And opened, Head Agent Leroy Jethro Gibbs stepped out and into his team’s workspace, carrying a cup of his morning coffee. Most NCIS agents came in at 9 AM, but today was unusual, as Director Vance had asked him to come in early regarding a new case.

A case that had only just come to the attention of the US government, the Department of the Navy, and now, NCIS. Gibbs took a sip of his coffee before opening a secure line to Director Vance on his computer. It didn’t take too long for Director Leon Vance to appear on the screen.

“Agent Gibbs.” Director Vance said. “We’ve got a major situation.”

“Hit me.” Gibbs responded. “If it’s big enough that I need to come in at this time, I think the “major” part goes without saying. What’s going on?”

“This is classified information.” Vance replied. “The US Government and the Department of the Navy are involved in negotiations with the realm of Equestria. I’m sure you read the briefing packet I sent you?”

“Twice.” Gibbs responded. “Did something go wrong?”
‘
“Very much so. Two nights ago, a squad of US Marines deployed to the Equestrian’s main naval yard under complete secrecy. Last night, I received word that one of them, Lance Corporal Derek Simmons, was attacked and nearly killed.”

Gibbs raised an eyebrow, showing a rare sign of surprise.

“As a result of the Nat-Sec concerns both sides have raised regarding this, Agent Gibbs, your team is front and center on this. You, Agents David, DiNozzo, and McGee, miss Sciuto, Dr. Mallard, and ME assistant Palmer are to lead the investigation.”

“What do I need to know?” Gibbs asked.

“I’m sending over briefing packages for everyone. I need to all to leave as soon as possible.” Vance replied. “Everything we currently know will be relayed shortly.”

“Understood.” Gibbs said, and as the line ended, Agents Tony DiNozzo, Ziva David, and Tim McGee entered the room and began to set their things down on their desks. Gibbs cleared his throat, successfully getting their attention.

“Don’t get too comfortable.” Gibbs said as he retrieved his gear before heading to the elevator. “Pack up and grab your gear, we’re moving out, so be in the garage asap.”

“What is going on, exactly?” Ziva David asked as she, DiNozzo, and McGee did as Gibbs advised, but each was very confused while doing so.

“No clue.” McGee replied. “Tony?”

“Well, it's probably something big.” DiNozzo replied as they joined Gibbs in the elevator, which began to descend. “We didn’t even get to sit down…is there something big going on, Boss?”

“Bigger than you think, DiNozzo.” Gibbs said, giving DiNozzo a well-deserved headslap as they entered the garage. To the surprise of the other Agents, Dr. Mallard, Palmer, and Abby were all packed up and waiting for them in a separate NCIS-marked SUV.

“I’ll explain on the way.” Gibbs said simply as they entered another SUV. “So pay attention, we’ve got quite a drive ahead of us.”

====

“So…” DiNozzo mused as the two NCIS SUVs headed down the forested road towards a large complex building. “Equestria, huh? How long has this been a thing?”

“Don’t ask me, DiNozzo.” Gibbs responded. “I just got the news this morning from Director Vance.”

“So, just to get everything straight…we’re going through a portal…to another world…populated by ponies and other fantastical creatures…because a Marine Lance Corporal who was already there…got attacked and left for dead?” Ziva said, not sure if Gibbs was playing some kind of joke on the team.

“That’s pretty much it, yeah.” Gibbs replied as they parked, and began to unload their gear. After a security check, they were escorted to a large warehouse-like building. Inside was a strange machine that was hooked up to what seemed to be an old, antique mirror made from white and blue crystal.

“Are we all set?” Gibbs called out to the technicians, who responded that they would be transported in about thirty seconds, and they were advised to take a deep breath and hold it at the ten-second mark.

“Umm…why would we…” McGee started to speak, only for Gibbs to glare at him and he quieted down. At the ten-second announcement over the PA, everyone present took in a deep breath and held in. Then, they were enveloped in a flash of white light as the portal activated.

====

The NCIS Agents’s vision soon returned to normal, and they found themselves inside a room made from marble, that was also designed like a more modern greek temple. There were windows, but they were tinted heavily.

“So…Equestria, huh?” Tony said, feeling rather underwhelmed. “Doesn’t seem like much to me.”

“That’s because you haven’t seen anything substantial of our realm just yet.” Said a female voice. The agents turned to see a pair of Equestrians with a horn and wings walk into the room, escorted by four other Equestrians wearing purple and gray armor.

“You are the NCIS agents that my sister mentioned would be leading the investigation at the Naval Yard?” The first one asked. “A pleasure to meet you. I am Princess Luna, this is Princess Twilight Sparkle.”

“Likewise.” Gibbs replied. “Leroy Jethro Gibbs, team lead, NCIS. This is Tony DiNozzo, Tim McGee, Ziva David, our medical examiner. Dr. Donald Mallard, his assistant Jimmy Palmer, and our forensics expert Abby Sciuto. Where are we heading to?”

“Follow me, we’ll show you all to the train station.” Luna replied. As the agents followed the Equestrians out of the room, their vision was suddenly obscured by the sunlight. As it cleared, they could see they were in a large garden area, with the Royal palace to their left, and an overlook on the right.

“DiNozzo, was it?” Luna asked. “If you would like to see one of the best views of Canterlot, now is your chance. The balcony over there is available.”

Tony walked over to the aforementioned overlook, and saw, in full, the majority of Canterlot, and the city and plains that surrounded it. He, after regaining his higher brain functions, quickly fumbled for his smartphone to take a few photographs of the view.

“Got something to say now, DiNozzo?” Gibbs smirked as Tony returned to the group.

“Yeah, uh, sorry.” Tony replied sheepishly. “Nice place you’ve got here.” He added, which in his mind, would hopefully keep Gibbs from giving him a head-slap. However, there was no such luck.

“Did you just…smack the back of his head?” Twilight asked, now very confused herself. “Are you even allowed to do that?”

“Don’t worry, GIbbs does that all the time, and not just to Tony.” Ziva replied flatly as they all moved together towards the exit. “And only if it’s deserved.”

“How reassuring.” Twilight deadpanned.

“On that note, let us be off!” Luna interrupted all too hastily. “I believe the train is waiting for us at the station, so it’s best not to delay at the moment. I’d imagine it would be detrimental to your investigation if you weren’t there as soon as possible.”

“You’re right about that.” Gibbs said, and any further conversation was postponed as they exited the palace, and headed down the street to the train station. Despite the Lunar Guards’ best efforts, the presence of seven strange beings did not go unnoticed by the citizens. There were plenty of stares, whispers, and gawking done at the agents as they passed.

Luckily, the presence of two Princesses and the Lunar Guards reassured the locals that everything was under control, and they were not accosted in any way during their walk.

“I take it they’ve never seen a human before?” McGee whispered to Twilight.

“Not in the slightest.” She replied. “We didn’t even know your kind existed until a few weeks ago. I actually don’t know enough of the details to tell you more, seeing as I wasn’t here for the first set of meetings. I live in Ponyville, which is about an hour west of here.” Twilight added, seeing McGee’s confused expression. “I usually come to Canterlot only if it’s really important or if I’m directly summoned.”

“That’s odd.” McGee mused. “I mean, if something were to happen here and you didn’t learn about it in time, that would be a problem.”

“I agree that it is an issue I need to work on, but I do have a way for sending messages to and from where I live in a timely manner.” Twilight responded as the group entered the train station. On a separate track was the train that would take them to their destination, as two other Lunar Guards stood by the doors.

After a quick check that the agents had everything they needed, and a show of their badges, the group sat down as their gear was loaded into the luggage car.

“So, it’ll be about two hours before we reach the naval yard.” Princess Luna said as the whistle blew, signalling their departure. “If there is anything you’d like to talk or ask about, now is the time. There are also refreshments in the forward car should you find yourself in need of them.”

“Thank you.” Gibbs replied. “So, what can you tell us right now about what happened? Do we have any leads?”

“I did receive a copy of the report filed by the two ponies who found your injured marine.” Princess Luna said, handing GIbbs a packet of papers that were sealed with the Equestrian royal crest. As the other agents gathered around to analyze the documents, Gibbs stepped aside, heading for the forward car.

“Is there something you need?” Twilight asked, getting up from her seat and catching up to him.

“Just going to get some coffee, if you have it here.” Gibbs responded. “Did you need anything?”

“We do have it, and honestly, that sounds good to me right now.” Twilight admitted. “‘Shall we?”

“Let’s.”

As the train continued towards its destination, the presence of the sea-salt in the air slowly became thicker, and it wasn’t long before sea-birds could be seen in the distance. It almost seemed if as they were beckoning or welcoming them on their imminent arrival.

Author's Note

Surprise, surprise.

I know I did an NCIS crossover some time ago, but I didn’t really have a plan for it or how it would progress. Now, things are different, and for the first time I actually planned out the ending of a story, rather than seeing where my writing takes it.

I hope you enjoy!

Next chapter - The Agents arrive at the Naval yard and begin their investigation, including their interview of the injured Lance Corporal…

Chapter 1 - The Preliminary Investigation, Part One

Royal Equestrian Naval Yard

Entrance Area

"I'm impressed." Gibbs noted, as he, his team, Princesses Luna and Twilight, and four Lunar Guards exited the train and took in the monumental sight before them. "I didn't think this place would be this big."

"We'll take that as a compliment." Princess Luna replied. "It took five years to build this naval yard. I was not present for the opening ceremony, however. My sister told me of the festivities that occurred when I returned from exile."

"Exile?" Abby asked. "What do you mean by that?"

"I was sent to the Moon for over 1000 years, and I only returned four years ago." Princess Luna replied. "It's a long story, and I owe Princess Twilight and the other Elements of Harmony for my return, but…I suppose now is not the best time to regale you with it."

"I would certainly like to hear it when you have the chance." Dr. Mallard smiled. "It sounds fascinating!"

Princess Luna gave Ducky a grateful smile, and as they entered the Naval Yard, three Equestrian sailors, one of which was in an admiral's uniform, approached the group.

"Admiral Fairgale, Lt. Blue Steel, Ensign Bright Sky, this is Agent GIbbs and his team." Princess Luna said. "They've come from the Human realm to aid in the investigation of the attack on Lance Corporal Simmons."

"It's a pleasure to meet you all." Fairgale said, shaking Gibbs's hand. Fairgale was moderately built, with a gray coat and a bright blue mane, which was kept in a ponytail. "Would you prefer to see the scene of the attack or the medical wing first?

"Both." Gibbs replied. "Tony, take Ziva and see if our Lance Corporal is up to answer any questions. McGee, help Ducky and Palmer process the scene."

"Very well." Fairgale said. "Blue steel, please show them to the medical wing, and Bright Sky, to the scene. I ordered that the entire section be cordoned off with a magical shield, so everything should be exactly as it was the night of the attack."

"Good." Gibbs said. "Let's get to work."

====

As Ducky, Palmer, McGee, and Bright Sky, alongside Princess Twilight, approached the shielded section of the wall, the Princess of Friendship used her own magic to take the barrier down.

"May I ask what exactly the shield was needed for?" McGee asked.

"It's a temporal dome spell." Twilight replied. "It locks everything inside the field into a state outside of time. Essentially, everything was flash-frozen the way it was when the attack happened."

"Impressive!" Dr. Mallard complimented. "Well, so far, I know that a bladed weapon was used, one with a rather long blade. These gashes in the stone wouldn't be present if the injury didn't penetrate the body. Adding to that, there's also blood inside the gashes."

"Huh…" Palmer said, taking a look at a strange scorch mark in the ground, which was shaped like four small imprints. "Someone was playing with fire here."

"Not exactly." Princess Twilight replied. "That's a spell-scorch, a sort of burn mark that's left behind when powerful magic is used improperly. Think of it like a glass of water being jostled, and some of the liquid splashes out."

"So our attackers were Equestrians." McGee noted. "That does beg the question as to how many of the sailors and command staff here knew about human Marines being here?"

"As far as I know…" Bright Sky spoke up. "It was only Princess Luna, the admirals in charge, and a few select lieutenants that knew of what was happening. I was told this by Blue Steel shortly before we found Lance Corporal Simmons. It was top-secret, and I'm certain Princess Celestia kept it quiet, even in a place like Canterlot."

"Why would that be the case?" Ducky raised an eyebrow.

"Let's just say that gossip, rumors, and unfounded information tends to spread quickly among the citizens of the capital, even more so when nobles are involved." Bright Sky said. "I would know."

"You're a noble?" Princess Twilight asked, surprised.

"Yeah, my dad, Horizon Line, is in the nobility." Bright Sky shrugged. "He's one of those types that doesn't particularly like big social events and formal gatherings. Although, he was actually impressed to hear that I wanted to join the Equestrian navy. Said it was a good way to see the world."

"I can agree with that point of view." McGee said, looking over to the street, as something shiny had caught his eye. As he slid on a pair of sterile gloves, he soon found it to be a polished silver cufflink.
"Looks like our attackers left something behind." he called out, and Princess Twilight came over to see what it was for herself. "Appears that it was cut off cleanly instead of torn from whatever it was sewn onto."

"That makes sense." Twilight said, examining the cufflink using a magically-conjured magnifying glass, then something snagged her attention. "There's some kind of engraving on it."

"What's it say?" McGee asked.

"Looks like an old Equish script, and unfortunately, I can't read it without a translation book." Twilight sighed. "Old Equish, back in the forming of Equestria, was the backbone of our modern language, but it was so complicated to write and speak that Princess Celestia personally had the entire language recomposed from the ground up. In fact, I've only ever seen it on things belonging to really old noble families."

"We'll need to hang onto this, then." McGee said, placing it in an evidence pouch. "How'd you know only old noble families use it, though?"

"A few weeks after I was crowned, I was invited to a party at a noble's estate outside of Canterlot." Twilight replied. "It wasn't a bad party, but eventually I needed a break, and I found myself in that estate's library, analyzing what artifacts they had present."

"Did you know anyone there?" McGee queried as Ducky and Palmer finished their analysis of the scene.

"No, it was all Canterlot nobles. There was a nice stallion about my age that I did share a dance with, but only because he seemed rather lonely." Twilight added. "He told me his name was Aether Trail. We talked in the library until it was time to go, since he's also a bookworm like me."

"He seems like quite a gentleman." Ducky commented.

"He certainly was, and I wouldn't mind meeting him again." Twilight blushed slightly, before composing herself. "Anyway, we should rejoin the others. I'll raise the shield I took down earlier."

After Twilight finished doing so, she, Bright Sky, and the three humans headed back towards the central plaza, where to their surprise, Gibbs, Ziva, and Tony were waiting for them.

"How's Lance Corporal Simmons?" Twilight asked.

"Well, for starters, he was able to answer all of our questions, and the doctors said he should be back on his feet in a day or two." Gibbs replied. "Thing is, whoever attacked him wasn't alone."

"He says he was blinded by something before it happened, but he could still hear and smell everything around him." Ziva added, consulting her notes. "He says that there were at least two other males based on the voices he heard, and one of them had a very distinct cologne or perfume applied. It apparently smelled like roses and fresh pine, according to Lance Corporal Simmons."

"So, we find the perfume, we find our attackers." Twilight reasoned. "I take it that's the good news, so what's the bad news?"

"The bad news is that every single Equestrian here has a confirmed alibi or uses that kind of perfume or cologne." Tony added. "So, back to square one?"

"I wouldn't say that just yet," said Admiral Fairgale as he approached. "I've just received word from Princess Celestia about a troubling development that happened right before the attack. Somepony managed to break into the Princess's office in Canterlot."

"Was anything taken?" Gibbs asked.

"Every single piece of correspondence from Earth and Equestria regarding the arrival of the Marines, the contract for the collaboration project, and the details for the public reveal." Fairgale reported. "There's no sign of who would be responsible, but there was a detail that stood out. A strange scent of…"

"Let me guess, rose and fresh pine?" Ziva finished, and the admiral nodded. "Whoever's behind this break-in is also involved in the attack on Lance Corporal Simmons."

"Then we're heading back to Canterlot." Gibbs said firmly. "Princess Luna, mind telling your sister that we're coming?"

"Of course." Princess Luna nodded. "Seeing as taking the train again would take too long, allow me to teleport us all there. Your friend Abby should also be waiting for us. Is everyone alright with that?"

There were several voices of approval, although DiNozzo seemed a little unsure, and McGee seemed a little too excited at the prospect. As Princess Luna and Princess Twilight charged up their horns, and the group vanished from sight in a flash of blue and lilac energy.

Author's Note

Update!

I got back into watching NCIS, and this came about as a result. Also, expect more Abby in the next chapter.