The Master Chief decides to activate the Halo under construction at the Ark to destroy the local Flood while sparing the galaxy at large. They follow Covenant forces through a portal to the Ark, where the Arbiter kills the final surviving High Prophet, ending the Covenant. Where does the arbiter kill the High Prophet? Thel ‘Vadam (the Arbiter) doesn’t enter into the story in Halo 4 but he does still lead a powerful Covenant remnant faction which is a de facto ally to the UNSC. He is ultimately killed by the marine John Forge in a climactic battle at a Forerunner installation.
The Arbiter acts as the primary enemy of the game, charged with the destruction of humanity by the Prophet of Regret.