At the start of the novel, Number 117 John is a child on the playground of the Elysium City Primary Education Facility No. 119. Dr. Halsey observes John to decide if he is a potential candidate for her project to turn humans into super-soldiers—into Spartans. Number 117 is abducted from his school and put into the training program to become a Spartan.
John spends years of his life training as a Spartan. He undergoes the augmentation process Dr. Halsey has invented to give John super-human strength, speed and more. John emerges as the leader of the Spartans. When the Spartans go on training missions, they all look to John as their leader and to provide them with commands and information on how to perform the mission.
As the years go by, John remains the Spartan leader. Eventually, he is sent, along with four of the other Spartans of his choosing, on their first real mission. John successfully leads the Spartans through completing their first mission. The second real mission John and his Spartans undertake is keeping the planet Reach from falling to the aliens, the Covenant.
By the end of the novel, John has not saved Reach from falling to the aliens. He ends up on a vessel that encounters a ring floating in space instead.