During the fight for Reach the last line of defense for the humans is represented by the "Super MAC" (Magnetic Accelerator Cannon) platforms in orbit around the planet. Faced with the knowledge that these massive weapons are the only thing stemming the tide of alien warships, the Master Chief (Spartan-117) sends a team of Spartans to the surface, in order to protect the MACs' planetside fusion generators... at all costs. This defense action however results in an ultimately futile gesture, as Covenant ships bombard the surface of the planet with plasma, glassing most of the planet, and forcing the remaining battered Spartans to flee underground and find Dr. Halsey, with whom they stumble upon an incredible discovery: a mysterious Forerunners' artifact that seems to be imbued with the power of bending time and space. The humans retrieve the object and hide from the Covenant who are looking for this very artifact and then await a Spartan retrieval force.

Picking up from where the game left off, the Master Chief and Cortana are stranded in space. Laden with valuable intel and a handful of survivors rescued from the destruction of the Halo construct (among them Sergeant Avery Johnson, the only man who survived Flood infection), they plan to return to Earth and do so by infiltrating a Covenant flagship, Ascendant Justice.

Once they get the ship mostly secured, the humans resolve to return to Earth with accounts of what happened on Halo and for the first time, a Covenant warship. The technological benefits for the human race would be enormous and might help win the war. Ascendant Justice's first jump is back to Reach, in line with The Cole Protocol. Because the Protocol dictates that a captured Covenant vessel must be searched and stripped of all tracking devices before going to Earth, the crew decides to leave the Ascendant Justice in orbit around Reach and return to Earth using a human warship. The Master Chief however has one more reason for visiting Reach: as the Spartans' commanding officer, Spartan-117 is anguished by the orders he gave his team that he felt were tantamount to a death sentence. The Master Chief wants to scout Reach seeking a closure, or even better, survivors.

Upon arrival in Reach's star system, the Chief's team picks up a signal fabricated by the Spartans in their training days (the hide-and-seek tune "Oly-Oly-Oxen-Free"); a remnant of Spartans had survived Reach, along with a handful of UNSC survivors as well as Vice Admiral Danforth Whitcomb, the "Deputy Chief of Naval Operations", who has armed the anti-planet "Nova" nuclear mine, a weapon that will either turn Reach and the Covenant invasion force into dust, or destroy wherever the Covenant takes it if they decide to do so. While investigating on Reach, the Chief also discovers Dr. Catherine Elizabeth Halsey and the rest of the living spartans with the Forerunner artifact, which appears to have bent time so that the Chief and Cortana could rescue Halsey and the others. While this is going on planetside, Cortana finds out that the Covenant have discovered the location of Earth and are about to deploy a massive assault fleet.

The humans must then fend off multiple attacks from the Covenant, who are determined to retrieve the Forerunners' relic in the Spartans' possession. Seeking a safe place to conduct repairs on Ascendant Justice, the UNSC forces rendezvous with the rebels of the Eridanus asteroid field. While docked at the rebel base, Dr. Halsey sedates Spartan Kelly-087 and abducts her, bringing her to Onyx as depicted in the book, "Ghosts of Onyx".

With the knowledge the Covenant are en route to Earth, the Master Chief and his Spartans, determined to buy some time for Earth, decide to go to the enemy fleet's rendezvous point and disrupt its initial operations in a decisive "first strike". The Spartans successfully infiltrate the Covenant command and control center station, the Unyielding Hierophant, and with the help of a copy of Cortana, they are able to set the station to self-destruct. In spite of this effort, the Covenant forces are not crippled, but Admiral Whitcomb manages to trick all of them to follow Ascendant Justice toward the doomed space station, pretending the Forerunner artifact from Reach is aboard his ship. A few minutes later the Unyielding Hierophant is destroyed, obliterating the whole Covenant fleet, taking the Admiral and Ascendant Justice with it. Onboard a damaged UNSC frigate, John-117 and the surviving Spartans, along with Sgt. Johnson and Cortana, head back to Earth to warn the UNSC of the Covenant's upcoming invasion.

The book ends with a scene in High Charity, showing the High Prophet of Truth and the Brute Chieftain, Tartarus, discussing the loss of Halo Installation 04 and the fate of the "incompetent one", a fleet commander who failed to ensure the security of the Ascendant Justice, who turned out to be none other than the future Arbiter. The first moments of Halo 2 depict his subsequent trial before the Prophets at High Charity.