 Over the course of the game , the Covenant pursue , damaging the Autumn and leading its crew to wage a guerrilla war on the ring 's surface . The Covenant accidentally release Flood imprisoned on the ring ; to nullify the threat , the ring 's AI caretaker , 343 Guilty Spark , enlists the help of the Master Chief in activating Halo . Cortana reveals that Halo 's activation would mean their own destruction . Master Chief and Cortana instead detonate Autumn 's engines , destroying Halo and preventing the escape of the Flood . 
