In the first, desperate days of the Human-Covenant War, the UNSC has enacted the Cole Protocol to safeguard Earth and its Inner Colonies from discovery by a merciless alien foe. Many are called upon to rid the universe of lingering navigation data that would reveal the location of Earth. Among them is Navy Lieutenant Jacob Keyes. Thrust back into action after being sidelined, Keyes is saddled with a top secret mission by ONI. One that will take him deep behind enemy lines, to a corner of the universe where nothing is as it seems.

Out beyond the Outer Colonies lies the planet Hesiod, a gas giant surrounded by a vast asteroid belt. As the Covenant continues to glass the human occupied planets near Hesiod, many of the survivors, helped by a stronghold of human Insurrectionists, are fleeing to the asteroid belt for refuge. They have transformed the tumbling satellites into a tenuous, yet ingenious, settlement known as The Rubble–and have come face-to-face with a Covenant settlement of Kig-Yar . . . yet somehow survived.

News of this unlikely treaty has spread to the warring sides. Luckily for the UNSC, this uneasy alliance is in the path of the Spartan Gray Team, a three man renegade squad whose simple task is to wreak havoc from behind enemy lines in any way they see fit. But the Prophets have also sent their best—an ambitious and ruthless Elite, whose quest for nobility and rank is matched only by his brutality... and who will do anything to secure his Ascendancy and walk the Path.

The time line of this book takes place primarily in between 2535 and 2536, though the date is not mentioned frequently in the book, as it was in older Halo novels.

 Summary

The story begins with an attack by the Jackals in the Rubble, an Insurrectionist asteroid base which was constructed as a refuge base during the Siege of Madrigal. The Jackals attempt to steal navigation data from Ignatio Delgado and his friend Melko Hollister. Delgado is almost killed and Melko is killed, but the Spartan Adrianna saves him and orders him to keep Gray Team a secret.

Later, at Chi Rho, Lieutenant Jacob Keyes meets with Zheng and is transferred from teaching at the Academy to enforce the newly written Cole Protocol with the stealth frigate, the Midsummer Night. He returns to his ship with a new pilot, and Zheng in command.

Back at the Rubble, Delgado looks for clues, suspecting that someone within the Rubble's Security Council is attempting to sell the navigation to the Jackals, which would cause the Covenant to no longer require the Insurrection. Delgado learns of the Kestrel, a ship under the command of Bonifacio, a known smuggler and also on the Security Council. He meets Adrianna again in a small bar, Eddie's in the Rocks. They are both attacked by Insurrectionists, who overhear the questioning of the Kestrel. After being saved again by Adrianna, he is taken to the Spartan's ship to meet Jai and Mike.

Jai explains that Gray Team has been working to destroy any navigation data through the Cole Protocol, and that they are causing general havoc against the Insurrectionists. As Delgado leaves, he is instructed to find out more about the Security Council leak.

Back on the Midsummer Night, Jacob Keyes attempts to enforce the Cole Protocol on a civilian freighter. When the Lieutenant and a group of ODSTs board the freighter, the civilian captain detonates a bomb in a container, killing many ODSTs. Later, Keyes and the ODSTs are force to leave the ship by exiting through a hull breach they created because the freighter was rigged to blow the moment the Midsummer Night is within the blast proximity of the freighter. Keyes leaves first, taking the armor of an ODST and jumps into space, using his rifle to maneuver. Fortunately, Keyes leaves and is able to contact the Midsummer Night. However, the Insurrectionists on the civilian freighter blow up the ship to kill as many of the escaping ODSTs as possible. Keyes is eventually recovered and along with most of the ODSTs despite the dramatic explosion.

Meanwhile, on Sangheilios, a Sangheili Kaidon, Thel 'Vadamee (Arbiter in Halo 2 and 3) wakes from his sleep to be attacked by assassins sent by the Vadam Keeps Council to test their leader. The Kaidon easily disposes of the assassins and meets with the council, demanding to know who sent the assassins. Thel then disposes of an elite elder, who attacks him. After the quick fight, Thel then tells the elders that he was sent by the Prophets to a human colony, Charybdis IX.

The Midsummer Night arrives at Charybdis in order to prevent a group of Insurrectionists from gaining a crate of plasma rifles and plasma pistols. Lieutenant Keyes and the Major go planetside to meet with an ONI group.