Master Chief was only six years of age when The UNSC government took him and 70 other children for life long training. In his place they left a flash clone to be a placeholder for his parents without them knowing. His first name was John but, was assigned number 117 for the duration of his training. He was determined to be as near to a perfect human being as it is possible to be and so fit to undertake the physical and mental training necessary to become a Spartan II super soldier. Like the other candidates John was strong and swift and brave, but innate luck was what set him out from the other Spartans. This quality was noted by Dr Hallesy at the outset of the selection process and it was because of it that John was chosen to test the new Mjolnir armor that the Spartans were to be issued with.
The Spartans were trained under CPO Mendez for a total of eight years. In the first two years they undertook physical ,intellectual and weapons training. When the Spartans where eight years old, they were sent on a training exercise. The Spartans dropped from a pelican dropship over an area of wilderness. Each had one piece of the map leading to their extraction zone. The twist to the exercise was that the last Spartan to make it onto the extraction Pelican would be left behind. John quickly realised that teamwork was the key to the exercise and rallied the other Spartans worked together to complete their mission. This showed that he had learnt from an earlier failure where he had abandoned his team in order to complete the objective. When the Spartans arrived at the vehicle they discovered that it was guarded by men under orders to prevent the Spartans from escaping. Once again John showed his leadership potential and organised the young Spartans to take down the guards and escape. He then ensured that all the others got on the Pelican before him, meaning that he would be left behind rather than any of them. However Hallesy was so impressed by his leadership qualities and willingness to sacrifice all for his team mates that he was not only allowed to come with them but was promoted to squad leader. At the age of 14, Master Chief underwent both physical and cybernetic augmentation (including Carbide ceramic ossification, Muscular enhancement injections, Catalytic thyroid implant, Occipital Capillary reversal, Superconducting fibrification of neural dendrites, and Nural implants). Only 32 of the 70 children in the Spartan program survived the augmentation process
Subsequently Master Chief was assigned to a team of Spartans. He grew close to them and they had many successful missions. When the alien race known as the Covenant attacked the Earth homestead of Reach and took massive casualties, Master Chief and his squad became the humanity's last hope. In the first few fights, Master Chief and his fellow Spartans were slowly separated by death. Most notably was John friend Sam, who was forced to stay behind on a Covenant ship to ensure that a bomb detonated after he took a plasma round for the chief and breached his suit. On Reach the Spartans were assembled to undergo a suicidal mission to capture the Covenant Prophets and end the war. Here John was selected by Cortana, a UNSC smart AI. Her design was copied after doctor Hallesy who originally took interest in Master chief as a boy. She was supposedly killed fleeing from a battle aboard a space ship. However she was in fact going underground to escape persecution by ONI, the UNSC's special operations branch. Reach was attacked before the mission could get underway and the Chief escaped on board the Pillar of Autumn with Cortana.
When the ship was crippled during a battle with a superior Covenant fleet the Captain, a decorated war hero by the name of Keyes, crashed the ship on a strange ring world. After several skirmishes with Covenant forces Cortana discovered that the ring world was called Halo and was of religious significance to the Covenant. After the release of the flood the Chief was recruited by a robotic entity know as 343 Guilty Spark to activate Halo and destroy the parasitic life form. Guilty Spark also told the Master Chief that he was the Reclaimer, son of the Forerunners. He was prophesized to activate the ring. The Chief quickly discarded his remarks. What he failed to mention was that activating the ring would wipe out all sentient life in the universe in order to prevent the flood from spreading. Fortunately Cortana managed to stop John and together they decided to stop Guilty Spark. After tearing the command codes out of a Flood infected Captain Keyes they flew to the Pillar of Autumn's crash site and overloaded its engines. Destroying the ring and the Covenant ground forces.
Master Chief and Cortana captured a Covenant ship and rescued the survivors of the Spartan project on Reach before heading back to Earth. Here they were attacked by the Covenant Prophet of Regret, who had followed the instructions of a sacred prophecy and come to Earth looking for Forerunner artifacts, unaware that it was the human home world. After a short but bloody battle, in orbit and on the surface, the Prophet performed a slip space jump and disappeared, closely followed by the In Amber Clad with the Chief on board. When the ship dropped out of slip space it quickly became clear that the Prophet had discovered another Halo. The Master Chief went into action on the ring worlds surface to find and kill the Prophet while Miranda Keyes, Captain Keyes' daughter, tried to prevent its activation by getting to the Index before the Covenant.
The Chief was successful in his mission but was knocked unconscious when a Covenant ship glassed the area in an attempt to kill him. Miranda on the other hand was captured when the Arbiter, a Covenant holy warrior, arrived to claim the index. The Chief was sent to find the Index at the Covenant city of High Charity by Gravemind, the hive controlling mind of the Flood as the Covenant were under the misconception that activating the Ring would ascend them to the next plane of existence. The Prophet escaped on a Forerunner ship, heading for Earth and the Chief followed, stowed away on the massive vessel. Unfortunatly he was forced to leave Cortana behind as a safe guard against the Flood taking control of ships capable of slip space travel. He promised to return for her but she remained skeptical. When he is asked what he is doing on a Forerunner ship, Master Chief replies that his is going to "Finish the fight."
After being captured on board the Prophet of Truth's ship and subsequently escaping the Chief fought in the Battle of Voi, clearing the way for an aerial assault on the Prophets fleet. Which had been busy excavating something under the African desert. As the human ships attacked a massive portal opened above the ground, through which the diminished Covenant fleet fled. After the arrival of a flood infected ship containing a message from Cortana landed in the area, the Master Chief was forced to once again ally himself with 343 Guilty Spark. In her message Cortana said that the portal lead to another Forerunner installation called the Ark, which would allow Truth to activate all seven of the Halo rings dotted throughout the universe. Now working with the Arbiter who's race had seceded from the Covenant. The Chief and his allies followed Truth through the portal and engaged his troops. Victorious in all engagements the Chief was able to stop Truth from activating the rings, allowing the Arbiter to kill him. Unfortunatly they arrived to late to save Miranda Keyes, who was shot in the back by Truth while she tried to kill herself and Sergeant Johnson. AS only a human could activate the Ark and they had both been captured. The Gravemind chose this moment to make its play and betrayed the Chief, trying to infect him and the Arbiter. After fighting his way into a Flood colony the Master chief rescued Cortana and started to implement a plan to stop the Flood. Using the index from the first Halo the Chief activated an incomplete ring, that would destroy the Ark and the Flood with it. However Guilty Spark went rampant, killing Johnson, when he realised that the plan would destroy the under construction Halo. The Master Chief destroyed him and tried to help Johnson, but it was too late. The old sergeant told John,
"Send me out, with a bang."
Before passing him Cortana's micro chip. The two activated halo and escaped in the ship that had brought them to the Ark. Unfortunatly the portal collapsed while they were going through it and left them stranded, beyond the blast radius of Halo but in the gulf of empty space beyond the galaxy. Cortana predicted that it would be several years before they were found and so the Master Chief froze himself, telling her that she should wake him if he was needed.