During the early days of the Human-Covenant war, Mawikizi was retired and lived in Burundi on Earth, but was forced from retirement by the UNSC, who pressed him back into service and ordered him to lead their battle fleet. He fought the Covenant in intense battles on three worlds, losing each time. At the end of each battle, Mawikizi had to be forced to leave the planet, even as it was being glassed. As his fleet was being pushed back daily, he planned a last stand at Chi Rho. His command center on Chi Rho was Camp Patmos. He admired then-Lieutenant Jacob Keyes for his successful defense of the UNSC Meriwether Lewis and personal bravery during the battle.
In 2535, he had Lieutenant Jacob Keyes, Major Akio Watanabe, and Commander Dmitri Zheng brought to Chi Rho. Mawikizi considered Keyes a good tactician and thought it wasteful for him to be a teacher at Luna. He offered Keyes the opportunity to command the customized frigate UNSC Midsummer Night, but also agreed that they were to go on a mission for the Office of Naval Intelligence. He also had Jeffries transferred from the Destroyer UNSC Armageddon's Edge to Midsummer Night at Keyes' request.
- Halo: The Cole Protocol (First appearance)