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The answer to that is in the Halo book Contact Harvest when humans had first contact with the Covenent. The first meeting was between humans and brutes, however along the way a grunt attacked a member of Harvest's militia, killing the solider who was able to let some shots lose with his rifle, it was these shots which alerted everyone at the meeting and kicked of the war between the covenant and humans. At some point after the brutes had killed at least half of the militia and the rest of the militia had evacuated with most of the nearest cities populations, the covenant heirachs would have heard of the new threat known as humans. After consulting a captured "oracle" or monitor, the prophet heirachs were told that the humans were sacred, the prophets decided to keep this information to themselves and declared war on humanity wanting the complete annihilation of humanity. Thus the first human-covenant war started. The second human-covenant war started because there were still some elites, grunts and jackals who still believed that the Halo rings and shield planets built by the forerunners would propel them on the "great journey" led by Jul M'dama this "Storm Covenant" found requiem and kicked off the second war by engaging Sierra-117 and marines of the UNSC's INFINITY. This war is currently still raging even with the description of requiem