Having now obtained what he needed to cement his status as a war hero, the ruthless officer betrayed Task Force 141 in an attempt to destroy any links to his treacherous actions including his connection to Allen's death so he could bring Makarov down himself.
He betrays them because he wants to personally avenge 30,000 casualties killed by a nuclear bomb five years earlier. The soldiers killed there were operating under him, both Army and Air Force.