he taked a pelican with l.t haverson polaski and locklear and escaped the pillar of autumn. the legendary ending is a easter egg or something like that because johnson as escaped halo.
Sergeant Johnson was part of an operation with Captain Keyes, Bisenti, Mendoza, and Jenkins, as well as a large Marine team to destroy a Covenant weapons cache in a swamp. Upon aerial deployment, his fireteam faced absolutely no resistance until arriving at a locked room. A Marine hacked the door, forcing it to open, and the squad went inside. The Flood subsequently attacked them, as the weapons cache they raided was actually a Flood containment and research facility. As his squad fell to the onslaught, he was thought to have been killed by the Flood as well, as the last seen of him by the player was him being surrounded by Infection forms on Jenkins' helmet-cam. However, Johnson was a candidate in the Spartan-I project, ORION, and because of the augments and treatment, he developed a neurological disease known as Boren's Syndrome. Because of this dysfunction, the Flood was not able to infect him, and thus he escaped the containment facility. He linked up with Lieutenant Haverson, Corporal Locklear, and Warrant Officer Polaski at an unknown time, forming a rag-tag unit. They used Polaski's Pelican to escape Halo after a full-scale Flood outbreak had occured, and the Covenant forces had shifted their attention from rounding up the Human survivors to the containment of the Flood. Once the Chief destroyed the PoA's reactor and crippled Halo, he united with Johnson's squad via Longsword and then the events of the novel Halo: First Strike unfold.