 Halo 3 picks up immediately after , with the Covenant 's leader , the High Prophet of Truth , and the remaining loyalist Covenant uncovering a portal to the Ark on Earth . A battle rages on Earth between human forces , the Covenant , and a Flood @-@ infected army . Eventually , the Covenant is repulsed and flees through a slipspace portal , and the Flood is purged from Earth , though much of Africa has been devastated in the battle . 
