Following the Flood infestation of High Charity, the High Prophet of Truth led the remaining loyalist Fleet to Earth to complete what the previous mission to Earth had not. Little did he know that a Spartan-II had stowed away with him on board his Dreadnought. By the time Truth arrived at Earth, a full-scale battle in space and on the ground was underway between UNSC and Covenant Fleets.
After a slug-fest lasting several weeks, the UNSC Homefleet was nearly wiped out. However, the Covenant Loyalist fleet was also vastly reduced and focused on securing an enormous unearthed Forerunner structure near the ruins of New Mombasa. With the arrival of John-117, the remaining UNSC forces launched an assault on the area, sweeping aside all Covenant resistance and finally launching an all-out attack on the Prophet of Truth's Forerunner ship.
Unfortunately, even in-atmosphere MAC strikes proved ineffective against the Forerunner dreadnought, and Truth quickly activated Voi's portal and escaped. Events were further complicated by an unexpected attack by the Flood. Thanks to the timely arrival of the Sangheili, the Flood force was vanquished but not before Master Chief recovered a recording from Cortana, who had stayed behind on High Charity. Cortana's message told of a means to stop the Flood on the other end of the portal. A small fleet of Human and Sangheili forces was sent through the portal, leading them to the Ark, just outside the Milky Way galaxy. The Covenant Fleet above the Ark immediately attacked. Though the joint Human-Sangheili fleet was outnumbered 3-1, the battle ended in defeat for the Covenant Loyalist Fleet. Simultaneous to the space battle between Jiralhanae and Sangheili ships, UNSC forces were deployed to the surface of the Ark.
The final battle of the war was fought in December 2552 as Truth attempted to activate the Halo rings. Led by John-117, the Human forces, despite fanatic resistance managed to smash through the remaining Covenant forces on the ground. The battle was complicated by the arrival of High Charity. As the Flood began to spread, John and the Arbiter went on to thwart Truth, who died in mid-Flood-infection at the Arbiter's hand. John-117 deactivated the Halo Array and brought an end to that threat as well. With the Covenant forces completely shattered, Truth's death marked the effective end to the war. The Flood still remained a threat, but were destroyed by John-117, the Arbiter, Cortana and Sergeant Johnson by firing the Halo over the Ark, destroying the parasite and the installation. The Forward Unto Dawn managed an emergency slipspace jump, returning John-117, the Arbiter and Cortana back to earth.
After returning, an alliance and truce were agreed to by the Sangheili and Human forces. While some of the more zealous Sangheili fled on what ships they could find, the majority of Sangheili rallied behind the Arbiter, Thel 'Vadam, creating the Swords of Sanghelios.
To further strengthen ties, the UNSC and Swords of Sanghelios began joint operations with the focus on spreading the news of the fall of the Covenant and new alliance between humans and Sangheili to both human and Sangheili colonies, searching for the remaining Halo's to secure them, and searching for additional Shield Worlds and Forerunner artifacts. These joint operations saw Swords of Sanghelios warriors and Spartans working together as the beacons of hope for their respective races.