They want control of the Halo rings to destroy the universe, we are trying to stop them. They also roam the galaxy and burn any planet they can find to glass.
Well yes but why would they want to destroy the universe? any reason? nope?
CORRECT ANSWER: A Covenant Luminary, a device that detects Forerunner objects, mistook the humans of Harvest as Forerunners. The Covenant religion states that when the Forerunners fired their superweapons (Halo Array), they passed on into god-hood. This meant that the Covie religion was flawed. If the rest of the races found out, they would have broken away from the Covenant, most likely violently. In an attempt to save the Covenant alliance, the Prophets hid the truth and declared that the humans were heretics, infidels, people that defied a belief or religion; they ordered the complete extermination of humanity. They are not senselessly violent creatures. The Flood are the ones that want to take over the Universe, not to destroy it; they want to dominate all life.