The Flood is one of the non-playable factions in Halo Wars. They will be aggressive to both sides of a battle, and have the ability to take over structures from other factions. They are known as parasites that feed on living creatures, and are credited for eliminating the Forerunners during a war that lasted almost a thousand years.Halo Wiki: Halo Wars

The two major factions in Halo Wars are the UNSC and the Covenant. They are at war with each other, and the single-player campaign has players take control of the UNSC. The Covenant sees humanity as a heretic race, and wants to wipe them from the face of the galaxy. It is your duty as the UNSC to fend off the Covenant and make sure they don't get their way.

In addition to these three factions, there is also the Forerunner race to take into account. There are ancient Forerunner relics that the other factions can use to there advantage. The Covenant worshiped the Forerunners as gods, partially due to the massive complex structures they left around the galaxy, like the Halos.Halo Wiki: Halo Wars