On June 1, 2536, the Covenant finally broke into the Inner colonies. From this point on, the war ground on in a predictable pattern; costly victories on the ground for UNSC forces, and near total Covenant space superiority. The UNSC managed to deal a heavy blow to the Covenant in 2537 with the destruction of the Covenant manufacturing plant K7-49 in Operation: PROMETHEUS, and again during the Siege of the Atlas Moons in the same year. However, these victories were offset by the loss of New Constantinople, its colonies at Leonis Minoris, and the total destruction of the force of Spartan-IIIs deployed to destroy the Covenant base.
Throughout the 2540s, the UNSC was dealt ever greater blows with the death of the Spartan-II Sheila during the Battle of Miridem in 2544, defeat during the Fall of Arcadia and the loss of Paris IV in 2549. A major human success was Operation: TORPEDO in 2545, the loss of 298 Spartan-IIIs were considered acceptable losses by UNSC High Command. The Spartan-II Raid on the Third Fleet of Glorious Consequence also proved the Covenant Empire was overwhelmingly powerful, but not invincible.
Of the few wins in the 2540s for the UNSC was the Battle of Psi Serpentis in 2543. This battle became colloquially known as Admiral Cole's last stand due to the presumed death of Admiral Preston J. Cole. In addition to the alleged death of Cole, over 300 Covenant vessels, two fleets worth, were completely vaporized when UNSC nuclear missiles detonated inside the atmosphere of Viperidae, a super massive gas giant. This detonation spurred spontaneous fusion at the core of Viperidae, temporarily turning the super gas giant into a brown dwarf star. Cole's achievements in this battle alone were only rivaled by the destruction of Unyielding Hierophant and the actions of John-117 throughout the course of the war. A painting depicting the battle, titled "Admiral Cole's Last Stand" was created and by 2552, it hung on the wall of the HIGHCOM Facility Bravo-6 in Sydney, Earth. The battle was one of the most significant and strategically important victories for the UNSC in the entire war.
Towards the end of the war in 2552, the Office of Naval Intelligence was resigned to the fact that humanity may only have months left before the Covenant destroyed the remaining Inner colonies and moved on against Earth. To buy time, and perhaps survival, HIGHCOM ordered all available Spartan-IIs to return to Reach and leave on Operation: RED FLAG, a mission to locate the Covenant home world, capture a Prophet and force the Covenant into a cease-fire.