 Chief , Arbiter , Elites , Johnson , Keyes , and U.N.S.C. troops follow Truth through the portal , joined by 343 Guilty Spark , who aids the Chief as he has no function to fulfill after the destruction of his ringworld . During the ensuing battle between humans , Covenant , and the Flood on the Ark , Johnson is captured by Truth to activate the Halo rings . Keyes tries to intervene , but is killed . Master Chief and the Arbiter , aided by the Flood , kill the Covenant " prophet " of Truth and rescue Johnson . After finding out that the Ark is constructing a replacement for Guilty Spark 's Halo installation , Master Chief decides to fire the unstable Halo , destroying both the Flood and the Ark . After finding out about their plan , Guilty Spark kills Johnson and tries to kill Master Chief , but Master Chief destroys Guilty Spark and activates the Halo . Master Chief and the Arbiter escape on the UNSC frigate Forward Unto Dawn , but the slipspace portal closes with Master Chief 's half trapped in space . After a memorial service on Earth for the victims of the Human @-@ Covenant war , the Arbiter and his Elite brethren depart for their home planet . The rear half of Forward Unto Dawn floats in deep space . Cortana activates a distress beacon and the Chief goes into hibernation . 
