While the backstory Phantom 2040 is exactly the same as the backstory of the television series, the video game does not specifically enact any of the series’ episodes but instead borrows elements from various episodes in the overarching story of the Phantom’s mission to stop Maximum, Inc. from dominating Metropia. The game follows primarily side-scrolling action elements. At several points in the storyline, players can make a direct choice about which path they take (in each case, the paths reconvene at the next chapter).
Every choice the player makes results in a unique ending, meaning over 20 different endings are available. A select few endings are classified as successful endings, while all others result in negative outcomes for the city of Metropia and present the player with the message “Try Again”. Phantom 2040 has a heavy emphasis on exploration. It is up to the player to locate the area’s objective or exit, and every area offers optional areas with restoration kits or weapon upgrades.
Some areas are locked by numbered gates that must be opened by destroying the remote lock of the same number, located elsewhere in that area (additionally, some locks can only be accessed if the area is reached by a secret underground network of sewer systems which connect every area). The area’s objective may include locating a keycard, dealing with a boss or simply finding access to the next area. The majority of areas can all be revisited at the player’s leisure anytime after they are unlocked.