In Fractured Soul 3D, players take on the role of interplanetary rogue, Jake DeSaul - a man with a checkered and mysterious past who must confront his demons in his desperate plight to escape an eerie and malevolent space station. As they progress through each level, the boundaries between dream and reality continue to blur as Jake faces a lifetime of regrets, hopes, dreams, and what might have been in his efforts to reconcile himself with his past.

In order to help Jake, players must blast their way through 20 exciting and brain bending platform levels spread across five distinct worlds - each offering a unique challenge including inverted gravity, damage, wind, ice, and underwater. Additionally, there are four shoot 'em up levels that also make use of the screen switching. Each level is timed and ranked to encourage replayability.