The story begins on the planet Jericho VII on February 12, 2535, and reveals the Spartans as a whole, as well as their purpose. As the seemingly unstoppable Covenant war machine moves into place to glass Jericho VII, Spartan Red and Blue teams are sent to prevent the destruction of the planet. The Spartans manage to kill a thousand Grunts and even destroy a Covenant air strike with fougasses. However, soon the situation in space deteriorates, and the Spartans are forced to retreat before the surface of Jericho VII is glassed.
The story itself begins with Dr. Catherine Halsey and Lieutenant Junior Grade Jacob Keyes on board the Han, a UNSC diplomatic shuttle. Their mission is to identify a potential candidate, John, for Halsey's Spartan-II program. Dr. Halsey finds John in a school playground in Elysium City, on Eridanus II, where she tests if he is good enough to be a Spartan. Using a coin, she tests John's reflexes by flipping the coin in the air and having him identify the side it will land on. John catches it and correctly identifies the side: the eagle. During this time, Halsey gives John the coin, which is later taken from him.
The plot then goes on to show in detail the brutal indoctrination and training regime that John and his fellow Spartans are put through. Chief Petty Officer Mendez trains the Spartan-IIs, showing them the many necessary virtues of a soldier (e.g. courage, teamwork, skill, etc.) while Déjà teaches them history, mathematics, and physics. After a daring training mission in the wilds of Reach, where the young Spartans regroup and escape with pieces of a map that they all put together and stole a Pelican back to base, where John-117 is made squad leader of the remaining Spartans. When the Spartans are fourteen, they undergo intense biological enhancements, such as effectively increasing their strength by three times, drastically increasing reaction times, making their bones practically indestructible, increasing blood flow to the eyes so that they can see in the dark, and other various improvements. However, of the 75 Spartans, less than half emerge still fit for combat; the rest died or were horribly disfigured by the augmentation progress.
The Spartans are then issued orders to capture Colonel Robert Watts, an Insurrectionist leader in the Eridanus asteroid belt. John leads a small team, which manages to capture Watts. John is wounded during this mission and is subsequently awarded a Purple Heart.
On February 3, 2525, first contact is made with an alliance of alien races that refers to itself as the Covenant. On that day, a single Covenant warship exterminates the entire surface population of the Outer Colony Harvest. Three CMA warships, the destroyer Heracles and the frigates Arabia and the Vostok, are sent to investigate this incident, initiate first engagement protocols and attempted contact, engage the Covenant ship in battle, and are subsequently routed. Only one, the Heracles, manages to return to Reach, having been badly damaged. By December of the same year, the UNSC has mobilized a massive fleet under the command of famed war hero Vice Admiral Preston Cole, with orders to reclaim the Harvest colony and stop the Covenant advance.
Cole's fleet manages a victory at Harvest, but at a high cost - two thirds of his ships are destroyed. Despite significant tactical brilliance on the part of Human commanders, Covenant technology guarantees a three to one kill/loss ratio in most space battles. One by one, the Outer Colonies fall to the onslaught and, by 2536, all have been destroyed.
To protect the location of Earth, the Vice Admiral Cole establishes the United Nations Space Command Emergency Priority Order 098831A-1, more commonly known as the Cole Protocol. If any Covenant forces are present, selective purges of databases on all ship based and planetary data networks are to be activated. When human forces are forced into retreat, they must not execute a Slipspace jump in the direction of Earth, or any major population center, even if this forces them to jump without the necessary navigational calculations (a "blind jump"). If such a jump is not possible, and if capture is imminent, the commanding officer must order a self-destruct. The on-board ship Artificial intelligence construct, normally imperative to navigation and tactical decisions, must either be destroyed or removed.
Due to the shortage of effective officers, Keyes is promoted to Commander and assumes command of the UNSC Iroquois. Shortly thereafter, he foresees a Covenant attack on Sigma Octanus IV thanks to a paper by Spartan Fhajad-084. His actions result in the destruction of a Covenant destroyer and two frigates as well as the routing of a DDS-class carrier with a daring maneuver dubbed the "Keyes Loop". This unprecedented victory against a Covenant force earns him a promotion to Captain and helps him to become recognized by the entire UNSC. Keyes and the Iroquois remain in the Sigma Octanus system to partake in the Battle of Sigma Octanus IV. He later returns to Reach, inadvertently disclosing the location of the planet to the Covenant via a homing beacon attached to the Iroquois. He is debriefed by an ONI council. Here he meets John-117 once again.
By 2552, many of Humanity's Inner colonies have been destroyed by the Covenant. In a move of desperation, ONI Section 3 orders the execution of a secret plan to capture a Covenant ship using the Spartans. The ship would be taken to the Covenant home world in order to capture a Prophet, one of the aliens' religious leaders, and then use the Prophet as a bargaining chip to negotiate a truce.
To aid the Spartans in this mission, an AI, Cortana, is created based on a younger Doctor Halsey. John is introduced to Cortana during a live-fire mission to test their capabilities working together, and they perform spectacularly. With Cortana's aid, John manages to overpower a full squad of Orbital Drop Shock Troopers, pick his way through a minefield, destroy automated chain guns, and even evade an air strike from a Skyhawk fighter, all of which are using live rounds.
Every remaining Spartan-II - with the exceptions of Gray Team, Kurt-051, Jorge-052, Maria-062, the original Red Team, and Black Team - boards a specially outfitted Halcyon-class light cruiser known as the UNSC Pillar of Autumn, which is under the command of Captain Jacob Keyes. The Pillar of Autumn moves out towards the edges of the system to make a Slipspace jump to begin the mission.
This plan, however, is interrupted when a massive Covenant fleet of 314 ships enters the Epsilon Eridani System. Captain Keyes orders the Pillar of Autumn back towards Reach, but John-117 convinces him to allow the Spartans to continue their mission by finding a damaged Covenant ship to capture and take to Covenant space. Reach's fleet, with about a hundred ships and twenty Orbital Defense Platforms on hand, engages the Covenant fleet, but takes massive losses. However, the Super MAC platforms manage to repulse the initial Covenant assault.
The Covenant return and land troops on Reach with the objective of destroying the generators for the Super MACs, the only things which are stopping the Covenant. At the same time, the UNSC realizes that the UNSC Circumference, a Prowler, is still docked at a station orbiting the planet of Reach just before its fall and has not initiated the Cole Protocol. John takes Linda and James to deal with the Circumference, while the rest of the Spartans are sent down to the planet to defend the MACs' power generators.
John's team crash-land their Pelican on the station which the Circumference is docked on and move towards the NAV data. However, James' thruster pack is hit by a Needler shard and explodes, sending James flying uncontrollably into space, where he presumably dies. John and Linda proceed to the Circumference, where they find Sergeant Johnson and his Marines, including Jenkins and Bisenti, also fighting to wipe the data. With John's help, the Marines are successful, but Linda is shot by five separate plasma blasts. The humans fall back to the Autumn; Linda is clinically dead because of the extensive wounds she receives, but is placed in a cryotube in the hope that she can be resuscitated.
The surface of Reach is also overrun. The Spartans who John sent to the surface are presumably overrun and all slaughtered. Without the generators, the Super MACs fall silent and are destroyed by the Covenant, who soon begin glassing the planet. The remaining UNSC ships are all destroyed, except for the Pillar of Autumn, as Cortana plotted an exit vector in compliance with the Cole Protocol, though not completely at random. She had decrypted Forerunner glyphs found by John-117 on Sigma Octanus IV. The NAV coordinates led the Pillar of Autumn to what the Covenant had been searching for: Halo, an extremely sacred Forerunner artifact. The book ends with Captain Keyes looking through view screens at the ring, asking Cortana to identify the object.