With the majority of the Outer Colonies glassed or abandoned, the UNSC faced an economic crisis. Some of their most important Agricultural Worlds had been destroyed, leading to widespread food shortages. On Charybdis IX, riots broke out. Meanwhile, Covenant forces began to encroach on the Inner colonies. In response, the UNSC issued United Nations Space Command Emergency Priority Order 098831A-1, "The Cole Protocol." No UNSC vessel could be permitted to lead the Covenant to Earth, or any other human population center. Furthermore, all movement through space was restricted to UNSC Navy vessels. Insurrectionist attacks increased in the face of what they perceived as a removal of their right to freedom of movement. This was to culminate in the discovery of Insurrectionists using Covenant weapons modified for human use from seemingly renegade Kig-Yar. Shocked, the UNSC saw this as a major threat to security. The Covenant viewed it as heresy that humans would modify their weapons, and as a result the Prophet of Regret dispatched Thel 'Vadamee to destroy the source of the modified weapons: The Rubble.
Fleeing from the Battle of Charybdis IX, UNSC Midsummer Night chased an Insurrectionist freighter to the Rubble and discovered that the Insurrectionists there had actually formed an alliance with a colony of Kig-Yar. These Kig-Yar supplied the weapons, and the Insurrectionists modified them. The crew of Midsummer Night, including its captain, Lieutenant Jacob Keyes, were captured, but later escaped and aided Spartan-II Gray Team and the Rubble's citizens stop an assault from the Kig-Yar leader, Reth, and 'Vadamee's forces. It later transpired that the Prophet of Truth had ordered the Kig-Yar to ally with the humans so that they could discover the location of Earth from stolen navigation data or through tracking devices in the weapons. Through this, the Covenant found two more worlds to attack.
By the time of the Battle of Jericho VII in 2535, most of the Outer Colonies had been destroyed.