Cave Story+ is an enhanced version of the original Cave Story. Compared to other versions it is the most complete version of the game contentwise. It has the re-drawn 2D HD graphics introduced in the 2010 WiiWare version, further enhanced for high resolutions along with a new menu design. It also contains remastered music in addition to new music. Both the graphics and the music can be switched for those of the original version. Both English and Japanese are supported as languages. The game now allows three concurrent saves and offers three difficulty levels with a specific outfit for Quote (yellow, red, and blue with a human look), unlike the original game. The difficulty level influences the enemies. The easy level halves their health and the damage they do to Quote. The normal level is identical to the original game and the hard difficulty level doubles all enemies' health and removes the health pick-ups. The game does not contain the 3D visuals from Cave Story 3D.
It contains the additional content of the WiiWare version with three additional game modes: Boss Rush, Curly Story and Sanctuary Time Attack. Entirely new for this version is the Nemesis Challenge. It starts the game with only ten health, the Booster 0.8 to hover for a short amount of time, and the Nemesis weapon. This weapon encourages the player to swap health for firepower, as upgrades decrease its efficiency in both power and range. After two power-ups the gun will only shoot rubber ducks and the only way to turn it useful again is by losing an upgrade by getting hit. That way, dodging enemies is encouraged over destroying them. Also new is the Wind Fortress, a new, challenging area based around jumping and hovering with only two weapons: Blade and Spur, vastly limiting the defensive options. This version also contains additional seasonal content based around Christmas and the holidays.