Though by all appearances a 3D-enhanced port of the original Space Harrier, Space Harrier 3-D actually features whole new worlds, enemies and bosses. The original Space Harrier had been released on the Sega Master System the prior year. As well as the 3D enhancements, several improvements were made to the graphics including reducing the flicker for the fast moving sprites, especially for the many segments that make up the bosses.
Though almost impossible to play without the stereoscopic 3D glasses, the game did feature a 2D mode. However, in order to unlock this mode, the game would have to be completed in its 3D mode first.