A brief description for the unwary.
The Covenant is a religious, government body of various alien species, and serve as the primary antagonists of the Halo franchise. The populace of the Covenant under the deceit of the Prophets, believe humanity is desecrating their religious beliefs, and wage war on them for "heresy." Unknown to the majority of Covenant however, the Prophets falsely created this ruse against humanity to maintain political power and to keep the Covenant from dissolving.
Full details are on Halo Nation.