John was born in 2511 and lived with his mother and father in Elysium city on the colony world of Eridanus II. He attended the Elysium City Primary Education Facility Number 119. As a child, John had brown hair, freckles, and a small gap between his front teeth. In a dream during cryo-sleep aboard the UNSC Pillar of Autumn, John recalled that his mother "kind of smelled like soap," and that she had "large eyes, a straight nose and full lips."
The would-be UNSC Marine Lieutenant Parisa was a childhood friend of John's who John once saved from drowning at Lake Gusev; John thereafter promised to marry and protect her. Parisa's father shot a photo of the two soon after that Parisa kept as a memento long after she thought John had died.
John was also friends with Ellie Bloomand Katrina during his childhood. Some nights, John would lay in grass fields with the girls and the three of them would look up at the stars together.
Dr. Catherine Halsey identified John as an ideal physical and mental candidate for the 150-strong preliminary pool of the SPARTAN-II Program when he was six: he stood a head taller than the majority of his schoolmates, had greater physical proportions, and possessed greater strength, superior reflexes, and an aggressive drive for success. When Dr. Halsey and Lieutenant Jacob Keyes visited Eridanus II in 2517 to study him, they were impressed with his intellect and luck. 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. John was the first candidate Dr. Halsey and Lieutenant Keyes studied. Later that same year, John and 74 other six-year-old children were "conscripted": they were covertly kidnapped from their homes and replaced with flash clones, all of which would later die of neurological problems stemming from the imperfect cloning process, covering up the kidnappings. John, along with the other candidates, was taken to the planet of Reach. Dr. Halsey informed them of the SPARTAN-II Program and how they would be "the protectors of Earth and all her colonies." The next morning John discovered his service tag, stitched into his training uniform, and his new name: John-117.
John began a new life. He trained with other Spartans under Chief Petty OfficerFranklin Mendez. For eight years he learned history, military strategy, weapons and received physical fitness training. Early on, he bonded with Kelly and Sam, who would become two of the few close friends that he would ever have.
John quickly proved himself to be one of the program's top candidates during his training. Both Dr. Halsey and Chief Mendez identified him as one of four emerging leaders within the Spartan-II group, along with Kurt-051, Jerome-092, and Frederic-104. Dr. Halsey most strongly expressed her belief in John by stating that he had the skills and natural ability to lead the entire Spartan-II group. However, Mendez disagreed and instead believed that Kurt would fulfill that role.
When the Spartans were eight years old, they were sent on a training mission in which they were dropped over a forest located deep in one of Reach's snow-filled mountain ranges and expected to get safely to their extraction Pelican dropship. The children also had instructions to leave the last child arriving behind lest they receive painful punishment; John-117 knew, however, that he could not do that. After telling the Spartans where to meet, the Spartans looked to him as their leader, a role he was initially surprised to receive but eventually accepted. When the group came upon the Pelican, it was guarded by armed men. Those men were actually UNSC Marines but were not in uniform; the Spartans therefore mistook them for a hostile threat. John showed early acumen in critical thinking and tactics, not wishing to take for granted that guards would be friendly toward them. He came up with a plan to take the men down, capture the dropship, and ensure the safe extraction of every team member, as he made sure he was the last person aboard. To do so he ended up hijacking the dropship with the help of Déjà and beat down the men with stones, causing severe injuries among the Marines. Chief Mendez was visibly displeased by John's having attacked his Marines and leaving no-one behind, but both Mendez and Halsey recognized John's initiative and promoted him to squad leader. Thereafter, despite other Spartans' rising in rank and at least a couple rising to lead their own teams, he remained the de facto leader of the Spartans as a whole.
John's leadership skills were correctly observed: the result from their mission clearly solidified his role as the overall leader of the Spartan-IIs. He also became the established leader of the Spartan-II Blue Team.
At the age of fourteen, John underwent the dangerous SPARTAN-II augmentation procedures. These procedures killed 30 and physically disabled 12 of the Spartan trainees. John was one of 33 Spartans who survived the process unscathed, while the rest who could still operate were moved to positions in the Office of Naval Intelligence. At only fourteen years old, John was said to have the body of an eighteen-year old Olympic athlete; the augmentation process hastened their reflexes, increased their strength, enhanced their eyesight, and rendered their bones nearly unbreakable. After their augmentation procedures, John and the other Spartans were transferred to the Atlas in order to recover in a microgravity environment. Four ODSTs confronted John during his first visit to the Atlas' gym; their sergeant then ordered the five of them into the boxing ring. In the ensuing fight, John killed two of the ODSTs, and left the others severely injured, an incident which quickly blossomed into major resentment for the whole SPARTAN Program throughout the Marine Corps. According to Major Antonio Silva, "people who invented John" orchestrated this incident in order to test the Spartans' augmentations.