The High prophets made a discovery linking directly Humans with Forerunners. Due to this contradicting their own ancient religion the High Prophets declared war on Humanity in 2525 and the Covenant fought the UNSC in (main) until 2553. There was an informal ceasefire due to the great schism and the Sangeheili joined forces with the UNSC to defeat the flood and stop the High Prophets and their lackies from firing the Halo array as they did not understand what they were. A splinter group, the new Covenant continues to fight with the UNSC in 2558 led by Jul'Mdama. You are doing a sterling job after OP has given up, thanks for the question. =}