Humanity and the Covenant first came into direct contact on February 3, 2525, when a Kig-Yar Frigate, the Minor Transgression, discovered a human ship that had dropped out of slipspace due to a problem with the Shaw-Fujikawa Translight Engine. The Kig-Yar raided that ship and another one. The Harvest shipping operations AI, Sif, found out about the raids as a result of the distress beacon from the ships (although she and an undercover ONI spook on Harvest thought that Insurrectionists, not aliens, were behind the raids). The spook set a trap for the Kig-Yar which resulted in a minor skirmish between Staff Sergeants Nolan Byrne and Avery Johnson and the Kig-Yar privateers. When the Covenant returned with another ship and a contingent of Jiralhanae, the UNSC proposed a meeting (via pictogram) to trade. The Covenant met the UNSC on Harvest, but were only interested in claiming the relics that the Luminary had detected on Harvest, completely oblivious that the humans were the "relics" in question. The meeting was botched after Osmo, a member of the Colonial Militia, was attacked by a nervous Unggoy, part of a second Covenant force sent to look for the relics. As a result, a firefight erupted between the two groups and the Covenant retreated back to their ship.
The Prophets declared Humanity to be an affront to their gods (later propaganda would declare humans had inhabited and "defiled" Forerunner artifacts and worlds), and called for a crusade against the Human species. The Covenant's final objective was nothing less than total genocide.
Unknown to all but the highest echelons of leadership, the campaign to exterminate Humanity was an attempt by the Prophets to maintain political and religious power. In truth, the Prophets had discovered Forerunner objects that the Luminary revealed on Harvest were actually Humans (which the Prophets interpreted as meaning that the Humans were descendants of the Forerunners, or possibly surviving Forerunners). Initially, the Covenant interpreted the glyph from the luminary as "Reclamation." The Forerunner AI 032 Mendicant Bias revealed that the interpretation was incorrect: the glyph meant "Reclaimer." The Prophets Regret and Truth realized that if the Humans were Forerunners, then it was possible to be left behind when the prophesied Great Journey occurred. This stood in direct contradiction to the Covenant religion. The Hierarchs, recognizing that this truth would destroy the Covenant, declared war on Humanity, hoping the truth would perish with their newly declared foe.
The first battle of the war was the extended, albeit one-sided, ground battle which took place on Harvest. The UNSC managed to delay the Covenant long enough to evacuate many of Harvest's civilians. Eventually, the Covenant used their capital ships to glass the planet's surface.
The Covenant continued to attack and destroy Humans wherever they were found, using their Luminaries to find Human worlds. Though the UNSC forces fought bravely, inferior technology made any victory difficult - dependent on strategic and numerical superiority, often with the aid of Spartans. Human armor, missiles, magnetic accelerator cannons, and crude slipspace technology were asymmetrically matched with Covenant energy shields, plasma torpedoes, energy projectors, and pinpoint slipspace jumps. The Covenant, fighting a war of extermination, did not need to commit to full ground invasions except in special circumstances. Covenant ships needed only to destroy human space-borne defenses, then reduce the planet's surface to glass with orbital plasma bombardments. Covenant troops were used to soften up UNSC ground forces, or hunt for holy relics. Over twenty-seven years, the Covenant whittled UNSC forces away through firepower and attrition.
Realizing the threat posed to humanity by the Covenant, the UNSC gave Vice Admiral Preston Cole the command of the then-largest fleet in human history with orders to retake Harvest. Cole retook Harvest in 2526, and then spent five years chasing the Covenant around the Outer Colonies, scoring victories at Alpha Aurigae, XI Boötis A, and Groombridge-1830. Meanwhile, the Covenant returned to Harvest, determined to recapture the planet. This led to a five-year long series of engagements on Harvest between the Covenant and the UNSC.