The WiiWare version of Cave Story is an updated version of the original game. The visuals have been updated to 480p definition, making the features sharper, and the game runs at 60 frames per second. The music has been remixed and there is an option to enable the original music as well. The in-game text has received a new English translation. The game now contains three difficulty levels, each with their own version of the character. On easy Quote takes less damage and enemies die quicker. On the hard difficulty level no power-ups or missiles are provided for the entire game. The game contains some seasonal content with additional costumes when the game is played on Christmas or Halloween.

Three additional game modes can be unlocked:

-Boss Rush mode pits Quote against all bosses in succession.

-Curly Brace mode replaces Quote with Curly as the protagonist. She is a female scout robot who can be met in the original story mode. Next to new dialogue and some cut-scenes, there are no changes compared to the original game.

-Sanctuary Time Attack is a time attack mode for Sanctuary, one of the most difficult sections of the game. It contains a lot of spikes and requires hovering to quickly navigate. Before entering the area Quote can pick up weapons.