He was held aboard the Truth and Reconciliation, a Covenant CCS-class battlecruiser, until he was rescued by Johnny and Cortana. Afterwards he led many attacks against Covenant emplacements across the ring.
He and his strike team unwittingly unleashed the Flood after Johnny located the Silent Cartographer and the Control Room, as the Covenant tricked them into thinking it was a weapons cache. The Flood attacked and assimilated the entire squad.
Keyes was assimilated into a Flood Proto-Gravemind, and held a valiant defense against its advances. He was mercifully killed by Johnny when he found him, in order to retrieve his neural implants. Keyes was remembered as a war hero, and was held in high regard by his superiors, his soldiers, and especially his daughter Miranda, who followed in his footsteps and joined the Navy, and played a pivotal role in the battles after her father's death.