Cave Story 3D is an enhanced remake of Cave Story and the first version for the 3DS platform. The most notable change is a revamped visual style, turning the 2D of the original into a 2.5D mode with the environment and the sprite characters remade in a high definition 3D polygon objects with dynamic lighting. It also has a distinct change in overall design with much more detail, replacing visual elements entirely, as a moving block now becomes an electric elevator for instance, water is animated, and basic platforms become statues. It also has a dynamic camera systems that zooms in or out automatically to give a better view. Optionally the game can still be played in a classic mode with the original 2D sprites in the 3D world.
The game's soundtrack has been remixed by Dustin Kulwicki and Danny Baranowsky. The overall game design is nearly identical, with small tweaks to make the platforming a little easier and with more health pick-ups. The base game is extended with four additional levels, based on designs of an unreleased beta of the original game. This new area also adds a few characters, a new weapon and references from franchises of publisher NIS, such as Prinny in the Western version and references to Crazy Climber, Dragon Slayer and Ikki in the Japanese version. Players can also unlock the Sanctuary Time Attack mode.
It does not have all the content of the previous versions however. The soundtrack player of the Nintendo DSi version is not included and it also does not carry over most of the additional content of the 2010 WiiWare version or the 2011 Cave Story+, such as the improved version of the 2D graphics. The new unlockable Wind Fortress area with the new enemies and bosses, and the Nemesis Challenge (Cave Story+), and the two game modes Boss Rush and Curly Story (Cave Story+ and the WiiWare version) are also not present.