The game revovles around a S.H.I.E.L.D. agent and you, as the player, would take control of the agent and guide him alongside the Marvel Super Heroes in a turn based RPG battle. The appearance of your agent is customizable. You can choose to be a male or a female agent and you can select his or her skin color, hair, and face appearances, and cusomize them to your liking. The agent is not as strong as the heroes during the early part of the game, and you will be assigned your default character class as a Generalist, later in the game you will be given the chance to Research and create a battlesuit for select classes like the Infiltrator, the Scrapper, the Bruiser, the Blaster, and the Tactician. You need to employ good strategy to survive and act as a supporter to your two accompanying heroes or choose to be a pure attacker or a combination of both. Either way the agent will be a flexible unit around the heroes who could only be of one class throughout the game thus making the agent an essential part of the team. The agent cannot be replaced unlike the heroes in the field of battle. The agents four skills are based on the items he has equipped and can be bought from the Shop, or dropped from missions.

The agents level affects the heroes too. The higher the level of the agent the tougher your heroes will be. The agent doesnt require training to level up unlike the heroes, but, the agents level determines what Research upgrades he can access to in the Research selection of the game. The Research helps the hero gain class suits, weapons, support consumables, and ISO-8.