Harper is notable as he was the one and only UNSC member who had power equal to that of Lord Hood. Despite Hood being Harper's superior in rank, Harper still had full right to disobey Hood's commands if he felt that his commander was going against the correct course of action. Despite this only being an insignificant loophole for Hood, he nevertheless decided that Harper was too powerful and decided to have him killed.
Despite Harper's massive successes against Covenant troops during the battle, his fleet was assaulted by Regret's carrier and its escort, and his ship came under heavy fire. Johnny was in the process of delivering a Covenant Bomb back to its rightful owner by flying out of Cairo Station's hangar when Fleet Admiral Harper's ship, the UNSC Marathon, flew over the Escort Carrier to deliver a payload of Longsword fighters. This order was given to Harper directly from Lord Hood, in order to grant Johnny access to the Carrier's power core.The Longswords blew a hole in the top of the carrier as planned, but not before the carrier itself unleashed its plasma projector on Harper's ship, gutting it instantly. It turned out that Hood had told Harper that the Carrier's weapons had been disabled as well as its shields, a direct lie, in order to get him killed when his ship was attacked.
What Hood did not predict, however, was that Harper did not die. When Johnny blew up the Carrier, the explosion damaged Cairo Station's sensors temporarily, leaving it unable to detect a single Orbital Drop Pod leaving the scuppered UNSC ship. Harper had escaped his assassination.
Fleeing to Earth, Harper crashed his damaged pod in Africa, and there he saw the true face of Lord Hood's tyranny. Harper had never set foot on Earth, only ever travelling from Reach to the Orbital Platforms. But when he saw what Hood's rule was doing to the last of humanity, he vowed to fight against it. The Empire of the Hood later displayed the 'evidence' of Harper's death to the UNSC High Command, who decided that Hood's analysis had been right and Harper was dead. However, Harper actually went on to lead the resistance against Hood's empire, eventually meeting back up with Johnny years later to plan Hood's death...