Gameplay is initiated for all characters at a common entry point: The Brainiac Harvester Ship. From there, based on the mentors and alignment, characters are assigned a series of missions. Missions are the main way to gain experience which is required to gain levels. Initial missions are assigned by the primary mentor and are unique to that mentor. As levels and renown increase, the characters skills are solicited by the other senior members of the JLA or Secret Society. Some of these missions are unique to alignment. Some parallel the opposing alignment and tell a story from either the hero or villain perspective. Each mission is composed of a series of sub-missions, some of which are chapters assigned by the mentor and some of the which are sidebars given by NPCs encountered in the game. At the end of a cluster of these submissions, a headline is generated and a video plays to terminate the mission set.
As levels increase, characters are contacted by senior operator for special team-based missions into specific locations or warrants and bounties are placed on specific high profile targets. In summary, PvE missions can be labeled as follows: