Phantom 2040 is set in a world where secret agent Phantom must stop the evil plans of Maximum Inc., a giant corporation that's developing new Biot technology. The Phantom faces off against the Biot threat, which are part of Maximum Inc.'s private army.
The gameplay involves navigating the Phantom through seven levels, completing mission objectives to progress. You can acquire and use limited ammo weapons, as well as gadgets like invisibility. The game features a mix of platformer and vertical scrolling shooter levels, with some parts requiring you to hack a computer in a mini-game to unlock doors.