The Covenant are a race of aliens that are controlled by a religious government and caste system. They control the Orion Arm of the Milky Way Galaxy, and are the main enemy of the UNSC in Halo Wars. They are waging a genocidal war on humanity, and in the main campaign mode of the game, it is your duty to destroy them to protect the human race.Halo Wiki: Covenant

Besides the two main factions in the game, there are also two neutral factions that will play a part in Halo Wars. The Forerunners are an ancient race of aliens that created many of the major structures in the galaxy, includes the Halos from earlier Halo games. There is also the Flood, who are considered a parasite and feed off of the biomass of other living creatures. The Flood once had a large war with the Forerunners, and now the Flood go around feeding off of the other lifeforms in the galaxy.Halo Wiki: [1]