Lost Brethren

by Mr Dorito

Rating: mature
Tags: Princess Celestia, Crossover, Tragedy, Main 6, Gore, My Little Pony: Friendship is Magic, Dark, Alternate Universe, Human, Other, Princess Luna, Original Character, Adventure
Length: 3694

A team of Spartans, Sangheili, and Jiralhanae crash landed on a beautiful, seemingly peaceful, unexplored planet. Things are not what they seem.

We did it, we finally ended the Prophet of Truth and eliminated the Loyalists. So why the hell did fate decide to land us in a planet full of mythical creatures. Why are there Humans too? This planet is supposed to be unexplored.
Disclaimer:
My Little Pony: Hasbro
Halo: 343 Industries
Inspiring Stories:
Your Human and You by MadMaxtheBlack
Your Human And You: Feet First Into Hell
Halo: A New Age by Mistasilentkiller and xpredatorx of Fanfiction
Obvious non canon story is obvious
Story is mainly Halo/MLP Crossover, but it's also a bit of a multicrossover.
This is my first fic. Criticisms are welcomed.

Published 2015-06-27 20:00:02 UTC
Last updated 2015-06-27 20:00:02 UTC

Prologue

February 2, 2375
In orbit above the planet Earth
Sol System
UNSC Endeavor
*sigh* “Why did I join the UNSC in the first place?”

On the observation deck of the Endeavor is 35 year old Captain Daniel Henderson. Sometimes he wondered, out of all the ships the UNSC has, why did he get stuck with a colony ship.

“You joined because you’ve always dreamed of going into space,” said a voice behind him. “You would talk nonstop of how you would explore the unknown and fight big bad aliens.”

“Oh, hey Adam, what are you doing here?”

“What, can’t a man say goodbye to his little brother?”

“No, I just wasn’t expecting you to be here. How’s the family?”

“Well Mom and Dad wish you the best of luck from Hawaii, Sheryl and Derick wanted to see you, and Madeline, Jonathan, and Chelsea are probably crying their eyes out.”

“Madeline is a tough woman, she’ll get over it. It’s only going to be 2 months. While I’m gone, please help Madeline with Jonathan and Chelsea.”

“Don’t worry, I will.”
There was a moment of silence until they saw another colony ship, the UNSC Voyager, pass the Endeavor.

“Beautiful ain’t it?” said Adam.

“Which one?The ships or space?”

“Both actually. You were right when you said space looks beautiful. The ships look beautiful too. Huh, can’t believe humanity would ever advance this far. Before, I actually thought humanity would be wiped out before we would colonize space. With all of the corrupted people in the world, I was afraid we were going to destroy ourselves.”
While Adam was talking, Daniel all of a sudden had a bad feeling.

“Are you alright Daniel? You don’t look so good.”

“Don’t worry, it’s probably nothing.”

“Are you sure?”

“Yeah, just ignore it.”

“Suit yourself. Hey where is your colony fleet going to anyway?” said Adam.

“Well, I was ordered to bring these colonists to a new planet that was named Tribute. Over 200,000 people are going to be brought there aboard the Endeavor, Voyager, Enterprise, Challenger, Ranger, Columbia, Gemini, Explorer, Soyuz, Apollo, Spatium, Manifest Destiny, Conquer the Stars, and Artemis.This is the biggest colony fleet ever assembled so far.”

“Tribute huh? Heard it’s a very beautiful place. I’ll probably bring everyone their one day.”

“Please, if anyone is bringing them to Tribute, then it’s gonna be me.”

“Hey, I heard about those new devices installed on all UNSC ships. What are they called again?” asked Adam.

“There called Shaw-Fujikawa Slipspace Drives. Everyone calls it the Slipspace Drive since it’s easier," replied Daniel.

“What do they do?”

“Well they create this giant wormhole which puts us in a pocket dimension and then teleports us to whatever coordinates we're put in.”

“What if something happened while you’re in slipspace?”

“I don’t know. You better ask the eggheads that question.”

“Hey, when you get back, go to Paris. There’s a bottle of brandy waiting for you.”

“Just you and me?”

“Yeah, just like old times. Remember when we were younger, we would drink a six pack of beer and drink on the roof of our old house at night.”

“Oh yeah, that went on for a few months before Dad found us and he gave us a beating. Ha, good times.”

“Anyway, I gotta go before the shuttle leaves without me. Be careful out there Daniel.”

“What, you don’t trust your own brother? I can take care of myself, don’t worry about me.”

With that Adam left the observation deck, unaware that this will be the last time he would see his brother.
1 hour later
Bridge of the UNSC Endeavor
“All ships report in," said Daniel.

Daniel listened as all ships in the fleet reported in.

“All ships, enter coordinates for Tribute and activate Slipspace Drives," ordered Daniel.

All of a sudden, all of the ships lost power.

“What the hell was that?”

“I don’t know sir. We just lost power," replied an Ensign.

Daniel looked out the window and witnessed the opening of a giant slipspace portal.

“Sir, all ships are being sucked into the portal!”

“Well get the engines online dammit!”

“I can’t sir, systems still aren’t responding.”

As the Endeavor and the rest of the fleet were being sucked into the portal, Daniel talked quietly to himself.

“Sorry Adam, looks like we won’t be able to share that bottle of brandy in Paris," Daniel said before he, along with everyone aboard, passed out.

February 3, 2375: Search for the missing fleet begins.
August 23, 2375: After 7 months of searching for the missing fleet, UNSC High Command calls off the search.

February 11, 2525: The UNSC makes contact with an alien alliance known as the Covenant on the planet Harvest. First Contact does not go well and starts the Human-Covenant War.

March 1, 2530: The Minor Prophet of Faith discovered the truth about humanity’s connections with the Forerunners from Mendicant Bias. She tells the truth to the leaders of each species in the Covenant and orders Arbiter Ripa Moramee to execute the High Prophets of Mercy, Regret, and Truth. There are those who are still loyal to the High Prophets and the Arbiter was only able to kill Mercy and Regret. Fleetmaster Jul M’dama saves the Prophet of Truth by bringing him to one of their Supercarriers. After heavy fighting with numerous damage to High Charity, Truth’s and M’dama’s Loyalist Fleet escapes.

March 2, 2530: The UNSC Colony of New Haven, located 22.4 light years from Sol, is visited by a Covenant Corvette. The colony thought they were under attack until they received a signal from the ship for a ceasefire. Admiral Preston Cole is sent with a hundred ships to confirm the ceasefire.

March 3, 2530: The Human-Covenant War is over and a peace treaty is signed to signify peace. The Sangheili and the San Shyuum offer humanity a place in the Covenant in which they accept and receive numerous Covenant and Forerunner technology with the Sangheili offering help to restore the planets they have glassed.

April 5, 2531: After a year, the UNSC wanted to change Covenant Caste System on how they treat other species. Eventually, they do and by orders by the leaders of the Covenant, all species must be treated equally. Also, the Covenant would be known as the Orion Systems Alliance with the capital being High Charity once it is fully repaired. The head of the Orion Systems Alliance would be a council headed by a Human, a Sangheili, and a San ‘Shyuum. Another council has been created which is called the Council of Admirals. The Council of Admirals job is to make decisions for joint operations and the defense of OSA home worlds and High Charity. Members include Lord of the Admirals Terrence Hood, Imperial Admiral Xytan’JarWattinree, Supreme Commander ThelVadam, Fleetmaster R’tasVadum, Admiral Jacob Keyes, Admiral Danforth Whitcomb, Fleet Admiral Preston Cole, and Fleetmaster Lepidus. The Office of Naval Intelligence is chosen to be the OSA’s Intelligence Agency.

June 7, 2531: The reconstruction of the Covenant into the OSA poses a challenge for all species. The Sangheili continue to be the military leaders and share this power with humanity. The San ‘Shyuum are the scientists of the OSA due to their extensive knowledge of Forerunner technologies, but also share that power with the humans. Politically, the San ‘Shyuum must also share power due to the fact that they are no longer the leaders of the Covenant. The Jiralhanae are still part of the military and have a rivalry with the Sangheili. The rest of the races are given a choice to join either the military or civilian sector. The Unggoy, Kig-yar, and Yanme’e chose both, the Mgalekgolo join the military sector, and the Huragok are put on engineering in all ships including in the UNSC.

August 15, 2534: The reconstruction is finally over and the Orion Systems Alliance is now the Galactic Government of the Orion Arm of the Galaxy.

May 3, 2535: Ever since the reconstruction, the UNSC learned a lot from their allies, but the subject that interests them the most is the Forerunners. Unknown to many, ONI discovered numerous alien technology in the colonies. They create Section 4 whose jobs are to learn from these alien artifacts and find out why only Humans can interact with the Forerunner technology.

October 21, 2535: Section 3 discovers a Forerunner artifact on the planet Harvest. The scientist team sent to Harvest, led by Professor Ellen Anders, discovers a holographic map of the galaxy which leads them to another Forerunner outpost on the UNSC colony of Arcadia. A small fleet, led by Captain James Cutter of the UNSC Spirit of Fire, is sent to Arcadia to assist the scientists there. Professor Anders discovers coordinates to a planet outside OSA space.

November 1, 2535: The small fleet find the planet and make landfall. On the planet, they discover an entire armada of Forerunner ships consisting of Dreadnoughts, Keyships, and Fortress ships. After a long debate, the Council decide to integrate the ships into the OSA Navies. The plan was to study them and use the ships as part of the defense fleets of OSA Home worlds, Fortress worlds, and, of course, High Charity.

February 15, 2540: In order to boost the OSAs military and intelligence capabilities, the UNSC create the Spartan Alphas. They were called Spartan Alphas due to the fact the members were Spartan IVs and it was seen as an extension of the Spartan IV program. UNSC officials picked Director Leonard Church to lead the project since he led Project Freelancer. Spartan Alphas have all aspects of a Spartan II, but have a higher risk of dying or horribly mutated during augmentations since the test subjects are adults. The first subject, call sign Dawnbreaker, was a success and the project continued. Out of the 234 test subjects, 117 survive. The 117 Spartan Alphas are now part of the Orion Systems Intelligence and are called Division 13 due to the number of Fireteams in the division. Director Church has been chosen to lead Division 13. Members of all races attempt to join Division 13, but only the Sangheili and Jiralhanae succeeded. Division 13 has a huge array of jobs which include exploring unknown planets, assassinate high value targets, protect OSA leaders, sabotage, spying, interrogation, etc. The planet of Sanctuary has been chosen as the primary HQ for Division 13. One reason for this is because Sanctuary is the first joint colony.

August 30, 2552: A UNSC patrol fleet, led by Admiral Andrew Del Rio, discovers a giant, planet-sized ring of Forerunner design outside of OSA space. Admiral Del Rio order images of the ring to be sent to Fleet Admiral Cole who then send it to the OSA council. The council decided to keep the information a secret and send scientists to the ring. The San Shyuum Counselor informs the council that the ring is a Forerunner construct called a Halo.

September 2, 2552: Science teams were sent to the Halo to study it and accidentally opened a chamber full of parasitic life forms which killed them all. Admiral Keyes and Supreme Commander Thel Vadam agreed to use nukes and plasma weapons on the infected are.

September 4, 2552: After bombarding the infected areas, more scientists were sent in to study the Halo. The UNSC sent in their own scientist led by the great Dr. Catherine Halsey. The scientists discovered what appeared to be a control room and a Forerunner AI who called itself 343 Guilty Spark. Through the AI they learned much about the Forerunners, the parasite known as the Flood, and the purpose of the Halo which is a weapon that wipes out all life on a galactic scale. They also discovered that there are 7 Halos altogether scattered somewhere. Guilty Spark could not divulge the location of the remaining 6 Halos, but told the scientists where they could find the Halos by finding the Ark through a portal on Earth.

September 7, 2552: The UNSC was surprised when they heard Forerunner technology was under their very noses for a long time. By using Forerunner tech, they found some readings underground between the city of Mombasa and the town of Voi.

December 27, 2552: After three months of digging, an artifact was uncovered which, when activated, creates a slipspace portal. Scientists believe the portal will lead them to the Ark. A small fleet led by Captain Miranda Keyes was sent in.

December 28, 2552: The expedition fleet comes out of slipspace over what they believe to be the Ark, a massive space station bigger than High Charity. Teams of scientists and their security detail are sent in to study the Ark. After a month, the scientists learned the location of the remaining Halos and a vast amount of Forerunner knowledge.
February 17, 2553: Fleets are sent to secure the remaining Halos.

July 12, 2575: The OSA Council decide to joint colonize worlds, the first being the planet Sanctuary and its capital, New Berlin.

August 10, 2575: Arbiter Ripa Moramee is assassinated by Covenant Loyalists who were then eliminated by High Charity Security teams. The Council announces the Arbiter’s death and declares August 10th a day of intergalactic mourning. Flags all over OSA territory are lowered to half-staff and people mourn the death of the Sangheili who ended the Prophets of Mercy and Regret. Supreme Commander Thel Vadam is right away announced as the new Arbiter by the Council.

December 18, 2584: A device of unknown origins has been discovered by science teams near the colony of Shanxi. Before the science teams could get closer to the device, a fleet of ships of unknown origin suddenly appeared near the device and opened fire on the shuttle the scientists were in, destroying it. Immediately, the unknown ships opened fire on the Shanxi Defense Fleet who angrily fired back. The crews of the Shanxi Defense Fleet could only laugh as the unknown fleet could not put a single scratch on their ships due to Forerunner shielding. The Shanxi Defense Fleet consisting of a CCS-class Battlecruiser, 3 Marathon-class Cruisers, 4 Halberd-class Destroyers, 2 CPV-class Destroyers, 5 SDV-class Corvettes, 5 Strident-class Frigates, and 8 Paris-class Frigates destroyed the unknown fleet of 30 ships except for 1 that jumped into FTL.

December 19, 2584: OSA AIs hacked into the surviving computers onboard the destroyed Xeno ships and learned about everything about this Citadel Council and their races including the locations of planets belonging to the Turians who attacked the Shanxi Defense Fleet. The OSA Council amassed an armada of about 1,000 ships near Shanxi to attack the Turian Fortress world of Gothis.

December 21, 2584: The OSA armada attack Gothis, completely destroying the Turian Defence Fleet and within the end of the day, OSA ground forces take over nearly 90% of Gothis thanks to ODSTs and Sangheili Spec Ops who wreaked havoc behind Turian lines.

December 22, 2584: The Citadel Council responds by sending the entire Citadel Fleet to retake Gothis. Once they reached Gothis, they arrogantly demanded that the OSA fleet surrender, believing nothing can withstand the firepower of the combined Citadel Fleet. Soon after their demands for them to surrender, 3 OSA fleets come out of slipspace around the Citadel fleet, completely surrounding them. The Matriarch commanding the fleet was shocked to finally see the size of the OSA ships up close, especially the CSO-class Supercarriers, CAS-class Assault Carriers, DDS-class Carriers, and the Infinity-class Assault Carriers. Right away, most of the Citadel fleet surrenders except for some arrogant Turian commanders who believe they can beat them. Their ships were destroyed, including the escape pods from those ships, sending a message to the rest of the Citadel Fleet to not mess with them.

December 23, 2584: Armadas of 3,000 ships are sent to the Citadel Home worlds, but are not given the order to fire. The Home world Defense Fleets could do nothing but watch and see what they would do. However, the Batarian fleet were the only ones to open fire, resulting in their immediate destruction. Meanwhile, an armada of 5,000 ships is sent to the Citadel with members of the OSA Council. The Citadel Council order their fleets to hold their fire and allow the OSA negotiators in. On their way to the Citadel Council Chambers, they were attacked by overzealous Turians and Batarians who were brutally disposed of by the OSA Security team which consist of members of all OSA races, Spartans, Sangheili Honor Guards, and ODSTs. The OSA negotiators drew up a series of demands to the Citadel Council, including full reparations for the OSA ground units killed or wounded during the assault on Gothis, scrapping 75% of the Turian Fleet, and the permanent demotion of the Turian Commander who attacked Shanxi. Also, the OSA demanded the Citadel to hand over any Forerunner technology they find and the OSA will, in turn, share Promethean technology. The Citadel Council reluctantly agrees and the armada returns to OSA territory.

January 1, 2585: Section 13 Fireteams Phoenix and Typhon infiltrate the planet of Elysium with a Prowler, which the Insurrectionists turned into a Fortress world with an armada guarding it. They assassinate the Insurrectionist leaders and leave behind a NOVA bomb. Once they were out of range, Fireteam Phoenix member “Chemo” detonated the bomb to celebrate New Year’s Day with members of the fireteams, all the while being videotaped and watched by military members stationed at Ft. Century in Sanctuary. This angers the OSA Council who call this act unnecessary and demands Director Church and the Council of Admirals to discipline them. Instead, they awarded them and gave them promotions. Meanwhile, the other Fireteams of Section 13 crack down on Insurrectionist and Covenant Loyalist activities and assassinate multiple leaders. The entire Insurrectionist and most of the Loyalist leadership was eliminated, but unfortunately, the primary target, the Prophet of Truth, eludes them.

February 13, 2585: One of the Forerunner Fortress ships was hijacked by sleeper agents within the ship on its way to Earth. Before Section 13 Fireteams could board the ship, it jumps into slipspace to an unknown location.

June 12, 2586: ONI discovers the location of the missing Fortress ship along with the rest of the Covenant Loyalist Fleet. The Prophet of Truth is there to lead the assault against Earth. Director Church immediately creates a plan for one of his Fireteams to detonate another NOVA bomb within the fleet. Meanwhile, a fleet is amassed on Sanctuary, led by Fleetmaster R’tasVadum, to wipe out any surviving ships that survive the NOVA bomb’s detonation.

Unknown Planet
June 13, 2586
In a cemetery near a huge castle stood a white, equine figure with wings and a horn in front of a tombstone.

“Hello Daniel, it’s been a long time hasn’t it? I’m sorry I haven’t visited in a long time. It’s just, I’ve been very busy lately. Remember when I told you about my sister Luna? She finally returned a few years ago. The new Elements of Harmony gave my sister back and I am eternally grateful for them. What else is there? Oh right, Discord freed himself from his stone prison. He caused some chaos here and there, but the Elements turned him back into stone. Then, there were some other incidents, like the Element of Kindness reforming Discord, the Crystal Empire returning, a magician taking over Ponyville. I forgot to mention. That area your people used to camp at is now the town of Ponyville. It’s a lovely place. I wish you could see it Daniel, you would’ve loved it. I still remember the old times when you would beat me at chess all of the time and pull pranks on each other. Oh, how I miss those days, that is until you saved me during that assassination attempt. Ponies never saw me as there god-like princess anymore. I’m just a figurehead now. It’s mostly the Council of Nobles that run this country now.”

Celestia started tearing up.

“It’s all my fault! I should’ve stopped them. I knew the Council and the majority of the population was calling for slavery, but I didn’t want to believe it. Now, Equestria is divided, at least not on the map. Most Unicorns supported slavery, the Pegasi hated the idea of slavery, and the Earth Ponies are divided. Many Pegasi formed groups to help Humans escape to Griffon or Minotaur lands. Cities like Las Pegasus, Manehatten, Phillidelphia,the Crystal Empire, and Cloudsdale outlawed slavery. Well, of course Cloudsdale would outlaw slavery; Humans can’t even walk on clouds! Appleoosa, Ponyville, Stalliongrad, Trottingham, and Canterlot still have pro-slavery laws. The Equestrian Army, Navy, and Air Force still thrive after you created them. The Army and Navy would capture or kill any runaway slaves on sight, but the Air Force has been known to help them escape. So far, only the Air Force and the Royal Guards pledge loyalty to me. Occasionally, Luna herself will come assist the Air Force or Royal Guards on saving any slaves, especially when members of the Army or Navy confront them. Nobles have been petitioning for Luna’s removal, but the Council knows removing her would cause issues with the Griffon Empire and the Minotaur Kingdom. After all, Luna and I are friends with the Griffon Emperor and the Minotaur King. Anyway, I need to go to another Council meeting. I’ve been petitioning for Humanity’s freedom, but I’ve only been supported by Councilor Fancypants. Head Councilor Blueblood could’ve removed him, but again, that would also cause issues with the Griffons and the Minotaurs. I have to go, I promise I will come back Daniel.”
On the tombstone Celestia walked away from read:

Here lies Captain Daniel Henderson
2340-2378 Human Calendar
Humanity’s Leader in Equestria and friend of Princess Celestia
Founder of the Equestrian Army, Navy, and Air Force
Sacrificed himself in the name of Humanity’s freedom

Author's Note

I felt like the timeline was necessary so you all can see the situation on this alternate universe. Story is currently an experiment. May continue depending on how many likes and dislikes this story has. Would like to thank my editor Requiem17