Two-player co-op mode has been enhanced with split-screen rather than forcing both characters to always be close enough to fit on the same screen, the game will seamlessly split when characters wander apart and merge into one screen when both players are near each other. All versions of Lego Indiana Jones 2 include a level creator where players can create their own levels and objects. The last level of each movie would consist of a major boss battle, where the player would need to defeat the movies' main antagonist. The vehicle levels involved the player using their vehicle to destroy enemy vehicles. The movies would also include a level that would have the player defeat a certain number of various enemies to complete the level.

Each movie is broken down into five levels, with the exception of Kingdom of the Crystal Skull, which was divided into three chapters with five levels each. Lego Indiana Jones 2: The Adventure Continues lets the player control a Lego figure in areas related to movie scenes and situations.

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