Bako 'Ikaporamee was a subordinate and assistant to the Prophet of Stewardship.
Thel protested since the fleet was military. Stewardship was captured during First Lieutenant Melissa McKay's raid on the ship. He made no attempt to hide his status as a Prophet, no doubt so they would take him prisoner rather than just kill him on the spot.
Thousands of years ago the Forerunner race were at war with the Flood and created the Halo space installations as a last resort to kill all other life in the galaxy so the Flood would starve to death. It is the goal of the Covenant to activate the Halos, which they mistakenly believe will send them on a "Great Journey" to godhood.
Being assumed Bako died when the Orbital Drop Shock Troopers boarded the Truth and Reconciliation. They captured Stewardship, the Marines possibly saw Bako as a hostile and killed him, or when John 117 destroyed Installation 04, or in combat with the Flood.