This is actually covered in the third novel, "First Strike". (The first, third, and fourth novels, by Eric Nylund, are quality works both from the "mighty Bungie game back story" and "good mil-sci-fi" perspectives. The second, "Halo: The Flood", is written by someone else and is basically a recap of mostly the lame parts of the game plus many diversions to new subplots about a human outpost that gets formed on the Halo and the activities of a few Covenant PoV characters.) He and a few other survivors made it off the Halo in a Pelican just in time and met up with the Chief after the game.

(Just how he survived the Flood attack that the Chief sees from Pvt. Jenkins' helmet camera is its own multi-layered enigma, with parts told in the "Breaking Quarantine" story from the Halo Graphic Novel, "First Strike", and a page of gallery art near the end of the HGN that suggests that the explanation given in "First Strike" is a smokescreen provided to hide the possible-truth that Johnson is secretly a SPARTAN-I.)