- last post: 01.01.0001 12:00 AM PDT
Okay, I've heard this question a lot. I'll clear it all up for you. Johnson has Boren's Syndrome, which disrupts the neural system. He went untreated and somehow survived. Since his neural system is disrupted, the Flood cannot find a resonance to match up with his neural system to infect him. He most likely fought the Flood until he was picked up by a Pelican.
By the way, in the Legendary ending, the Marine that is fighting with the elite is NOT Johnson. Bungie used his skin, but did not intend for that marine to be THE Johnson. Example: in AotCR, you see a group of marines near the Scorpion tank. "Johnson" is there, with the other marines. This CANNOT be Johnson, because in the book, "The Flood", Johnson is with Keyes in the swamp at this point, and the Flood has already been released.
That should clear up most questions dealing with Johnson.