In SR4, Kinzie becomes one in the simulation and Asha is one all the time. As a general rule, missions, strongholds, activities, and collectibles count toward 100% completion, but diversions, challenges, assassinations, vehicle thefts, stunt jumps, barnstorming, and property ownership do not.
100% Completion: An odd case, as each game tracks your completion, but not all content counts toward your percentage.
