In the beginning, Ben can stay an alien for a limited amount of time, but after defeating some bosses, Ben unlocks more powers for his aliens and even unlocks the master code, meaning he can stay alien for an infinite amount of time or switch between aliens without draining Omnitrix energy. Attack combos can be unlocked collecting Omnitrix points. Limited power boosts or invincibility can be gathered, as well as bonuses to make the Omnitrix recharge faster. Three Sumo Slammer cards are hidden in each main level, and once collected unlock features, such as movie clips.

After each level, Plumber ranks are rewarded, depending on how fast the player beats that level. If the player gets an A rank, you get a character view, usually a boss or a villain. In the main boss levels, a God of War styled button sequence allows players to execute a special attack at certain points.