As a kid on a playground, John was approached by Dr. Catherine Halsey and Lieutenant Jacob Keyes. He was the first potential SPARTAN-II recruit, standing a head taller than the majority of his schoolmates, he not only had greater physical proportions, possessed greater strength, superior reflexes, and an aggressive drive for success, but he had luck on his side. In a final test of his viability as a candidate, he was asked to determine which side an old coin would land on. He watched the coin as it flew in the air and caught it before it could land, correctly stating which side was face-up and which was the side of the eagle.
The Young Warrior
During his training under Chief Petty Officer Franklin Mendez he quickly proved himself to be one of the program's top candidates. After a successful training mission on Reach he was promoted to squad leader after proving his worth.
At the age of 14, all SPARTAN-II candidates underwent the dangerous augmentations which would provide them with the physique the SPARTANs would be known for. After recovering from this and a short skirmish with a couple of ODSTs, he was given the command of Blue Team to hunt down Colonel Robert Watts, the leader of the United Rebel Front. Following this, first contact was made with the Covenant on Harvest and John was given his first MJOLNIR armour, and was introduced with his new companion-AI Cortana. After a successful skirmish with a Covenant vessel, he decided to wear his new armour at all times.
27 years later, after many battles against the Covenant, John was given his Mark V armour on board the UNSC Pillar of Autumn near the planet of Reach. After Reach came under attack by a massive Covenant armada, John, with Linda-058 and James-005, were sent to destroy an unsecured NAV database containing massive amounts of data which would put humanity at great risk. During this mission, John rescued a couple of UNSC Marines, one of which was then-Staff Sergeant Avery Johnson. After the database was destroyed, John made it to the Pillar of Autumn and was put in cryo-sleep while Cortana took control over the ship. She plotted a course away from Reach, secretly basing the course on intercepted transmissions from the Covenant.
Once the ship had exited slipspace near a massive ring-shaped world, John left in a escape pod and started a number of skirmishes with the Covenant. During this fighting, the Covenant unwittingly set the parasitic Flood free, which would be a great threat to all life in the galaxy. Shortly after this, John-117 was convinced by the Forerunner AI 343 Guilty Spark to active the ring. The activation of the ring, apparently a superweapon, would have meant the death of all sentient life within a radius of 25,000 light-years. Stopped by Cortana, John then succeeded to use the Autumn's engines to destroy the ring.
The Fight Continues
Shortly after the destruction of the Halo Array, John reunited with his fellow SPARTANs to stop the Covenant's progress towards Earth, the location of which had been found. During the final confrontation of the Unyielding Hierophant with nearly 500 Covenant ships, the ship was blown up which resulted in the annihilation of 486 ships. The remaining ships later joined the Prophet of Regret's fleet towards Earth, the fleet attacked the Earthen city of New Mombasa. Here the flagship entered slipspace and led the following In Amber Clad towards a new Halo Array, Installation 05. Here Regret's plan was to ignite the ring as soon as possible, and dispatched a large fleet in order to achieve his goal. The fleet was accompanied by the holy city High Charity, which would later be infected by Flood spores present on the ring. John made his way onto High Charity and boarded the launching Forerunner ship, a Dreadnought, leaving Cortana behind.
John exited the ship from great altitude and crash-landed in a jungle environment, and with some Marine support he made it to the Dreadnought's landing site and looked on as a Flood-infected ship crashed on Earth. John later overloaded this ship's engine to destroy the immediate vicinity and thus the Flood infestation, any remaining Flood was later destroyed by the glassing performed by Rtas 'Vadum's ship. John made his way towards the UNSC Forward Unto Dawn and flew into a portal which had just appeared just above the Dreadnought. The portal lead to the origin place of all the Halo Arrays, Installation 00 aka The Ark.
The Ark, the Prophet of Truth had reached the Ark's Cartographer and was about to ignite all Halo Arrays in the Universe. John, helped by the Sangheili Arbiter Thel 'Vadam and a short alliance with the Flood, stopped Truth. The plan was now to destroy the Ark, by igniting the newly-made replacement for Installation 04, which had yet to be fully completed. But first headed to High Charity to rescue Cortana from the Flood's assault on her, after the rescue, John left together with Thel 'Vadam in order to ignite the new Halo Array. Shortly after starting the countdown to detonation, John and Thel 'Vadam made it towards the empty Forward Unto Dawn and fled towards the Portal back to Earth. However, while they were entering the Portal, it collapsed and split the ship into two parts. John drifted in space while Thel made it safely to Earth, John entered in cryo-sleep while Cortana monitored the situation and would wake John when he was needed.
Missing In Action
Four years, seven months, and ten days later, Cortana awakened John as they were heading towards the Forerunner Shield World Requiem. After crash-landing inside the planet and making scrambled contact with an apparent nearby UNSC ship, the UNSC Infinity, John unwittingly released the Forerunner Promethean Shadow-of-Sundered-Star, better known by his title as Didact. The Didact attacked the Infinity by pulling it towards the inner surface and locking it in place with a gravity well. John made it to the Infinity and made contact with UNSC Commander Thomas Lasky and SPARTAN-IV Commander Sarah Palmer. Together with Lasky, John went to destroy the gravity well and thus freeing the Infinity from Requiem. When the Infinity was free from all restrains, UNSC Captain Andrew Del Rio, Lasky's superior officer, ordered them to leave the planet and report back to Earth. Leaving the Infinity (against Del Rio's orders) to put an end to the Didact, Cortana was abducted while in Requiem's system. John was then approached by the preserved consciousness of the Librarian, another Forerunner, who told of the Didact's plans to the Composer against humanity. In order to combat the Didact effectively, the Librarian advanced his evolutionary process to render him immune to the Composing process, soon releasing him to fend off the Didact.
The Didact soon left Requiem by fusing his Cryptum with the Mantle's Approach and headed towards the location of the Composer, on a UNSC Research Station orbiting Installation 03. Here, Dr. Sandra Tillson inform John that it would be impossible to remove the Composer, so John decided to blow it up. But before he was able to, the Didact had located the Composer and used it to wipe out all the human researchers but only knocking John unconscious. John then boarded a Broadsword ship and succeeded in getting below the Didact's shield which entered slipspace. After the Mantle's Approach arrived at Earth, it was repeatedly shot by Infinity's MAC cannon in order to make an opening for John's ship. After insertion, John fought his way towards the Didact. Meanwhile, the Didact had successfully used the Composer to compose the population of New Phoenix. While the Composer was still composing, John encountered the Didact on a energy bridge and was about to blow them both up by igniting a nuclear warhead. The Didact initially stopped him, but Cortana manifested herself in the energy bridge and thus helped John overcome the Didact and ending him by exploding a Pulse grenade inside the Didact's armour. In an attempt to destroy the Composer, John ignited warhead and thus gave up his own life. His life was saved however by Cortana's final manifestation which protected him from the blast by given up her own 'life'.
Cortana's Loss and Blue Team
Cortana was gone, the hardlight aura around him flickered and faded and the debris of Mantle's Approach fell around him. Floating in space, he was picked up by a Pelican and brought aboard the Infinity. A brief confrontation with Lasky on the observation deck of the Infinity showed the now lonely soldier that he felt soldiers and people were two different things—and Lasky informed him that they were not. Suddenly John came to a realisation about himself. Being brought up as a killing machine had distanced him from being a human, and he now saw that he had distanced himself from almost every other person he had ever known. He recalled what Cortana had asked him earlier, about who out of the duo was the real machine, and finally he found himself an answer: it was him.
After his debriefing at UNSC High Command, John and Hood discussed John's future. Hood offered to promote him to the rank of Admiral, which was turned down by John, stating that "Admiral" didn't have the same ring as "Master Chief". Lord Hood then asked John if he wanted to serve in a consulting capacity with the rest of his Blue Team, John joined them, who were surprised to see him. Even though John was supposed to only consult, he quickly fought alongside Blue Team to track down Team Black, who were assaulted by Promethean Knights. Arriving there, Blue Team was ambushed by the Didact and his forces, dispatching them with ease. Even though the Didact had survived the Composer, here he was ultimately defeated inside the Composer's Abyss.
Absent Without Official Leave
Shortly after the Didact's defeat and the destruction of the Composer's Abyss, John is ordered by Lord Hood to have a break from military operations with Blue Team. Instead of taking the orders, John leads Blue Team on countless military operations when needed, drawing speculation of his mental state from ONI officials. An unknown amount of time later, John has gone missing and is considered to have gone AWOL. As a result of John's disappearance, ONI deploys a SPARTAN recovery team led by Jameson Locke.