In his early life, Johnathan lived in Elysium City, on the planet of Eridanus II. He was large for his age at the time, approximately a foot above his school peers. John had all the genetic markers set in Dr. Catherine Halsey's original study- he was as close to a perfect subject for the SPARTAN-II program as science could determine. He was a specimen of perfect physical proportion and stunning intellect. Dr. Halsey and Lieutenant Jacob Keyes went to his colony world to study him, and were quite amazed by his reflexes, and more importantly, his luck. To determine if he would be one of the ones chosen for the program, he was asked to determine which side a flipped coin would land on. He watched the coin as it flew in the air and caught it before it could land. John and the other 74 children unwillingly participating in the program were covertly kidnapped from their homes, and replaced with Flash Clones which later died of natural causes.
The Spartans were trained under CPO Mendez for a total of eight years. In the first two years the basics where trained, such as physical training, school and weapons training. When the Spartans where eight years old, they went on a training mission. The Spartans dropped from a plane over a wood. Each had one piece of a map. John assembled a plan to regroup at a lake and then piece the map together. The Spartans then advanced towards their extraction Pelican. But the men guarding the pelican weren't friendlies, so John came up with a plan to take them down and capture the Pelican. And because the last child was to be left behind, John made sure he was the last one on the Pelican. After this mission he was promoted squad leader of the Spartans.
MCPO John-117's first mission was against Rebels in the asteroid belt of the Eridanus System, where his home world was located. He was slightly wounded while leading his squad to capture the traitor Colonel Robert Watts, leader of the rebels. He received a Purple Heart after the mission.
Later on, he was briefed on the Covenant threat; he and his Spartans would fight at least the next 27 years against this new threat while employing the MJOLNIR Mark IV armor.
John's first battle against the Covenant was on a covenant ship just after they received the Mark IV armor. All Spartans launched with thrusters from a pelican. Each Spartan carried an Anvil missile with them to destroy the ship. Only three Spartans entered through a hole in the hull of the ship, which was put there by a MAC round. These Spartans were Sam-034 and Kelly-087. They succeeded the mission and blew up the Covenant ship, but lost Sam in the progress. This showed John that the Covenant could be beaten, but at a high cost. It was the first victory for the UNSC against the Covenant.
John fought in over 200 missions against the Covenant, amongst which was the Battle of Sigma Octanus IV, in which he detonated a nuclear bomb to clear all forces from the planet. It was one of few victory's for the UNSC. Amongst the other 11 Spartans in this engagement were James, Fred-104, Kelly-087, Joshua-029 and Linda-058. James got wounded in the mission by a Lekgolo. It was the first battle in which Lekgolo and Huragok were discovered by UNSC troops. A data crystal was also discovered in this mission which contained coordinates of Installation 04.
Other engagements in which John fought were the Battle of Jericho VII.
Though John fought shortly in the Battle of Reach, it was the difficult mission. While the majority of the Spartans went to the surface to protect the MAC generators, John, together with Linda-058 and James, where send
to a docking station where an unsecured NAV database was. If the Covenant obtained it they would find out the location of Earth. John was successful, but at a great cost. James was tumbled into deep space, either to be captured by the Covenant, but most likely to die of suffocation. He did manage to save four Marines however, including Sergeant Johnson. The four Marines and John with Linda's body then returned to the Pillar of Autumn in which they escaped Reach. Linda was then put in a cryo tube and was healed by Doctor Halsey after the Battle of Installation 04.
After many battles in the Human-Covenant War and surviving the Fall of Reach, he embarked with the Pillar of Autumn. The Pillar of Autumn was later attacked by the Covenant and was forced to crash land on Halo, Alpha Installation 04. In the midst of fighting the Covenant, Cortana discovered the secret of Halo while inserted into the computer in the Control Room of Halo; that it was a ring-shaped construct created by the Forerunners as a last line of defense against a new species of parasitic organisms called The Flood, which was released at some point by Captain Keyes and his marines by accident - a majority of the Covenant Elites and UNSC Naval Personnel and Marines who landed on Halo were infected by The Flood. Captain Jacob Keyes and a small group of Marines were the first humans to encounter the Covenant-released Flood; Captain Keyes was later captured by the Flood, soon after which he died. The Master Chief was then responsible for retrieving the Index for 343 Guilty Spark, a device which would activate Halo and destroy all Flood forms within a large radius. Later, Cortana informed him of the truth about the purpose of the installation (that it was a super weapon) that would destroy all sentient life forms, in other words, anything the flood could use as food. This led him to keep the Index from 343 Guilty Spark as long as possible. While being attacked by many Covenant, Flood and Forerunner Sentinels, he later made his way back to the Pillar of Autumn and initiated the destruction of Halo. Very few other members of the UNSC forces survived, notably Sergeant Major Johnson.
After the destruction of Alpha Halo, the Master Chief and Cortana floated in space in the Longsword he used to escape. He discovered three cyro tubes floating nearby, one of them containing Linda, and pulled them into the fighter. Soon after, the Covenant Flagship Ascendant Justice came into the system along with a few cruisers. A nearby Pelican dropship made its presence known and fired at the cruiser to distract it. John then linked the two vessels and brought its passengers aboard to the Longsword. There were seven others that helped in capturing a Covenant ship, rendezvousing with the Eridanus Rebels, and destroying the Covenant space station, Unyielding Hierophant. Linda-058 was another Spartan on the Pillar of Autumn, stored in a cryogenic state because of the body damage she sustained when she and Master Chief destroyed the data base containing the info needed by the Covenant to find Earth. Anton and Li were Spartans that died in an explosion after repairing the engine on the captured.
Also, two other Spartans, Issac and Vinh, survived the initial attack on Reach with Fred, Linda, Kelly, Anton, Li, Grace, Will and Dr. Catherine Halsey but sacrificed themselves by running into the middle of an entire battalion of Covenant troops and detonating an explosive. This selfless act destroyed the Covenant troops by more than half. Only Grace, Kelly, Will, Fred (Fredric), Linda and John were left. Dr. Halsey, head of the Spartan-II project sedates Kelly-087 and takes her on a mission that John and the others do not understand. John never knew of the others' fate. Prior to Halsey's disappearance, John faces a dilemma regarding the combat data on the Flood. Either he can give the regular data on the Flood, or give the complete data of the Flood encounter, which would condemn Johnson to death from ONI's subsequent experimentations.
After the First Strike operation, John made the decision to hand over the regular data and omit the explanation for Johnson's survival. After this, the Spartans that are still alive search for a way to stop the Covenant from reaching Earth, which has been discovered. John finds a way to do so, by using his remaining squad to destroy the Covenant Battleship known as the Unyielding Hierophant. Linda, John, Grace, Will, and Fred infiltrate the ship and quickly move forward to their positions. They cross the ship over a period of eleven hours and reach a temple, where a copy of Cortana warns them of a new guard known as "brutes". Linda leaves for a sniping position, and the other four Spartans slip into the temple. They are ambushed by Brutes, and John is nearly killed. He manages to kill the single Brute attacking him(in hand-to-hand combat), and kills the other Brutes his team is defending against. Grace however, is killed by the Brute Shot that chieftan Brutes used. John activates the failsafe on her Mjolnir armor and they proceed to sabotage the generator in the Hierophant. As the Spartans escape out a side door, the failsafe on Grace's armor activates, disintegrating several elites and many grunts. John, Fred, and Will are quickly spotted by three Banshees. As they flee, Linda snipes all three of the elites out of their cockpits, allowing the others to take the Banshees. John doubles back to retrieve Linda, who manages to snipe four more elites out of their Banshees while the Elites try to kill John. Linda is ordered to let John find her, and sends Oly Oly Oxen Free over her COM channel and places a nav marker on the HUD.
John finds her hanging upside-down off a catwalk, with a rope tied to her boot and another tied to the railing several meters above. She was hidden behind a brilliant light and in the depths of a deep shadow. She drops and lands on top of John, and they fly towards the place where Will and Fred are. They quickly escape, and arrive back at the Gettysburg. They see the Ascendant Justice being piloted by Vice Admiral Whitcomb and Lietenant Haverson straight towards the Unyielding Hierophant. Whitcomb discusses the Alamo and Thermopylae with John, then prepares to fight the Covenant off while the Unyielding Hierophant's fusion reactor detonates. Every one of the five hundred covenant ships maneuvers in right next to the Ascendant Justice, and the Admiral draws an SMG. The Admiral and the Lieutenant die, just as the fusion reactor explodes. The explosion annihilates four-hundred and eighty-eight ships of the fleet, leaving only a dozen badly damaged ships to invade Earth. John then leaves after witnessing Whitcomb's sacrifice, and arrives back at Earth with the last members of his team, Linda, Will, and Fred.
Chief's Mark V MJOLNIR armor was switched by technicians aboard the orbiting defense station Cairo to a Mark VI model. He attended a brief awards ceremony aboard the station. The ceremony was interrupted by Covenant boarders, which he repulsed. The Master Chief then briefly participated with defense in the First Battle of Earth. After confiscating a Covenant bomb that was intended to destroy the Cairo, he requests permission from Lord Hood to leave the ship to "give the Covenant back their bomb". Master Chief then drags the bomb into a Longsword hanger bay to launch it. The resulting depressurization of the hanger, causes him and the bomb to be flung into hard vacuum, where he manages to gain entrance into a Covenant Capital Ship's fusion chamber and detonate the bomb.
The Master Chief then hitches a ride on the UNSC In Amber Clad and lands in New Mombasa, East African Protectorate to combat Covenant landing troops. During the descent on board Pelicans, his dropship is shot down by the Scarab's main cannon. The Master Chief is briefly knocked unconscious and has to fight his way to the other Pelicans, with the aid of surviving Marines from his ship. After a rendezvous with Gunnery Sergeant Pete Stacker in the Zanzibar Hotel, in Old Mombasa, the Master Chief destroys Covenant units along the shore of the city as he chases the tracks of the Scarab. Once he arrives at the edge of Old Mombasa, he encounters a small group of Marines, whose platoon has been destroyed by the Scarab. The Master Chief receives a Scorpion Tank from Sergeant Johnson. After fighting through numerous highway tunnels, he arrives in various parks outside the main city, and after fighting through those, the Master Chief finally arrives in the city center, where a group of Marines, under the command of Staff Sergeant Banks were pinned down. With the assistance of the Marines and a large stockpile of weapons, the Master Chief manages to board and destroy the Scarab. The Master Chief is then transported to the In Amber Clad to intercept The Prophet of Regret's flagship. When the flagship starts to enter Slipspace, Commander Miranda Keyes is granted permission to follow it. The Master Chief and all on board the In Amber Clad are then brought to Installation 05.
At the Battle of Voi, Master Chief pushed through many loyalist forces as he made his way to what he believed was the Ark. In actuality, it was a only a device that would open up a portal to The Ark. Master Chief was able to destroy an anti-aircraft gun and allow Lord Hood's ships to fire upon Truth's defenses. Truth fled through the portal with his loyalists forces in a hurry, while the UNSC remained behind to determine their next move. Just as the Second Battle of Earth seemed to finish, a flood-infested Covenant warship crash landed in Voi. Master Chief was forced to, once again, battle the Flood and stop them from spreading. He learned that the only way to contain the Flood was to force the crashed Flood infested warship to explode.
During the battle, Ship Master Rtas 'Vadum came to aid the UNSC. He was able to fight off the Flood, as the Master Chief was sent on another task. The Elites informed the UNSC that the Flood had Cortana on that warship. Master Chief went to recover her, though it turned out to be a recorded message from Cortana. The Monitor, 343 Guilty Spark, took the message to the Shadow of Intent, where the Elites and the UNSC watched Cortana's recording. The Elites were able to stop the infestation by glassing half the continent of Africa, much to Lord Hood's displeasure.
Convinced of the reliability of Cortana's message, John-117 resolved to journey to the Ark while Hood tied down the remaining loyalist forces on Earth. John-117 accompanied a joint UNSC-Elite task force through the portal aboard the Forward Unto Dawn. Not knowing what dangers lie ahead, the Master Chief and his men journey into the Ark.
The Elites carried the Master Chief and UNSC forces through the portal, which led the team to the Ark. There, the team was determined to stop Truth from activating the seven Halos but first they needed to know how to find him. The UNSC sent down Pelicans to the surface of the Ark with intent to find the Ark's Silent Cartographer. Once they touched down on the Ark they encountered Covenent Loyalists establishing camps and AA batteries on the desert surface. The strike forces quickly disposed of these camps and successfully located a landing zone for the UNSC Frigate, Forward unto Dawn. Once landed the Chief took a squad of Scorpian tanks and marines to the entrance of the superstructure where the cartographer was kept. Once there the strike team encountered Covenant Wraiths and a Scarab.
After destroying these the squad soon found the cartographer and with it the location of Truth. He was housed within a Citadel protected by a barrier powered by a series of towers. After the marines evac. 5 pelicans and 3 Elite phantoms headed towards three of these towers which would lower a small portion of the shield allowing them access to the citadel. The Master Chief led a squad to one tower, The Arbiter to the second, and Johnson to the third, as Keyes and 'Vadum held off the loyalist starships in space.
Master Chief fought through many loyalist forces and eventually made his way to the top of the tower, where he deactivated part of the shield to Truth's location. The Arbiter soon followed, however Johnson was not responsive. He was overrun and captured by Truth. They needed Johnson to activate the rings, and so Master Chief and the Arbiter were sent to rescue Johnson and stop Truth. On the way there, the two fought Brute forces once more. After powering down the tower High Charity made a slipspace jump to the Ark, which brought the Flood into the battle as well, damaging the elite carrier 'Shadow of Intent' in the process. The UNSC forces battled their way to the citadel where they had to destroy two scarabs to progress further. Once they destroyed Truth's outer defensive forces the Arbiter, Master Chief and 343 Guilty Spark entered the citadel. When Master Chief and the Arbiter arrived at Truth's location, they realized they weren't close enough to stop him, since the elevator had been lifted. Miranda Keyes then forced her way into the edifice, breaking through the window with her Pelican. She managed to kill a Brute, but was soon surrounded. Truth killed Keyes with a Spiker when she hesitated to kill Johnson. Johnson, losing the will to fight, was then forced by Truth to activate the Halos. Master Chief and the Arbiter were finally able to make it to the top, and went after Truth. The Flood stopped them and the two made a temporary alliance with the parasite to stop the activation of the Halos. And so, the final Brute defenses were defeated by the Flood as Master Chief and the Arbiter reached Truth. Truth was infected by the Flood, and was soon killed by the Arbiter while the Master Chief deactivated the rings.
After the deactivation of the rings, the Gravemind revealed himself, laughing as he succeeded in preventing his own destruction. The Flood then attacked the Chief and the Arbiter. The attack failed and the two managed to escape. As they were leaving the citadel, Chief saw what seemed like a vision of Cortana. He was led to the exit by her, and it was revealed that a replacement for Installation 04 had been built, apparently by the Ark. Chief was set to once more detonate the Halo, but first, he took a detour to High Charity to retrieve Cortana.
On High Charity, the Chief battled his way through hordes of Flood forces, and eventually found his way over to Cortana's location, his visions stopped when he found Cortana and retrieved her. The purpose for finding Cortana was that she had the activation Index from the first Halo ring. The Master Chief needed the index to activate the new halo ring that was going to replace the one that Master Chief had destroyed in the first halo game. Once they were united, the Chief made his way back through High Charity and forced the Covenant City to explode. On his way out, Cortana detected a friendly unit which turned out to be the Arbiter. As High Charity was destroyed, the Flood was believed to be defeated.
He gave Chief the chip containing Cortana and the Chief activated Installation 04 as he headed out. Both Cortana and the Arbiter gave their condolences for the loss of Johnson to the Chief. The team fought the Flood as they escaped the Halo. Cortana remembered Johnson had come aboard the Dawn to get to the new Halo ring, and told the Chief to use Johnson's warthog to escape quickly. After evading death once more, John and the Arbiter made it onto Forward Unto Dawn and escaped the explosion of Installation 04.
A half ship then went through the portal, back to Earth. The other half didn't make it.
Unfortunately for Master Chief and Cortana, the rear half of the ship did not make it back to Earth. The portal wasn't able to sustain itself from the damage sustained to The Ark from the destruction of the Halo and closed as the ship was half way through. Only the front half, with The Arbiter, was able to make it back to Earth while the rear compartment of the ship ended up in the unknown. Cortana, relieved that John survived, explained this to the Chief, and that it could take years before anyone could discover their distress signal. Chief, whose armor's life support reserves were slowly draining, then put himself in a cryogenic chamber, to preserve himself as the ship drifted aimlessly in space.
Back on Earth, it was assumed that both the Master Chief and Cortana were lost, presumably in The Ark's explosion, since half the ship did not make it to Earth. A memorial was held in Forward Unto Dawn's crash site, for all those lost in the Human-Covenant War. The Chief's Spartan ID number, 117, was carved into the memorial by an unknown person or persons, and taped beside his number was the UNSC Master Chief Petty Officer of the Navy insignia patch.
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