Sgt. Johnson was a S-I. They were created under the "Orion Project" as the UNSC's/ONI's first attempt at creating supersoldiers. They weren't nearly as strong or fast as the S-II's but I believe they had a high mission success rate. Eventually ORION was disbanded and the soldiers were placed back in their respective branches, hence why Johnson is placed back in the Marine core to be later seen in the Halo games. This leads to the creation of "Boren's Syndrome". [spoiler]"Boren's Syndrome" is what they decided to name the altered genetics and side effects of augmentation to keep it hidden from the public. They detail it as high amounts of radiation that effect parts of the brain & central nervous/immune system if I remember correctly. Boren's Syndrome altered something about Sgt. Johnson's immune system allowing him to be the only marine NOT infected by the Flood when Master Chief finds Private Jenkins' helmet on Installation 04 showing how they're ambushed.[/spoiler] They go more into detail about it in the books with Halsey explaining it to Chief. She asks if they should sacrifice Johnson to try to find a cure to the Flood, possibly saving billions-trillions of lives, or if they should allow Johnson to live none the wiser. Master Chief picks the latter of the 2 options, which allows Johnson to survive until the end of Halo 3.