Phantom 2040 is set in a world where a powerful corporation called Maximum Inc. has created a private army known as the Biot threat. The player takes on the role of the Phantom , who must fight against this army and uncover the truth behind their sinister plans.
The game consists of seven levels, each with its own objectives to complete in order to progress through the story. Along the way, the player can acquire weapons, gadgets, and tools such as invisibility, which are used strategically to overcome challenges. The gameplay is a mix of platforming and vertical scrolling shooter elements, with some levels featuring mini-games that require hacking computers to unlock doors.