The character gains access to new areas as he powers up his weapons by collecting triangular experience crystals and solves various platforming puzzles.

Defeating enemies may yield yellow triangular crystals, which give experience points to weapons when collected, hearts that partially restore their health, or missile ammunition.

An army of robot soldiers was sent to the floating island on a military expedition, seeking to harness the Demon Crown as a weapon for wars on the surface.

[9][10] Shortly before the game begins, Professor Booster, the Sakamoto family, and various assistants formed a scientific party to research the island, but they became stranded when their medical doctor, Fuyuhiko Date, managed to acquire the Crown; he then forced the expedition to search for the red flowers.

[12] Sue attempts to rescue her brother Kazuma, but King, the leader of Mimiga Village, captures her and holds her responsible for Toroko's kidnapping.

After freeing him, they meet Professor Booster, who reveals that the Doctor plans to use the red flowers on Mimigas to create an army to take over the surface world.

While there, the player meets Curly Brace, a female robot who also has no memories of her past, and Jenka, an old witch who is Misery's mother and guardian of the red flowers.

The player scales the outer wall of the island to reach the Plantation where the Doctor is using the Mimigas as slave laborers to grow red flowers.

She is taken away before the player wakes up, but her letter reveals that the Doctor was a member of the research expedition that included Sue's family and Professor Booster, but he betrayed them once he found the Demon Crown.

The two are rescued by Kazuma and his Sky Dragon, while Momorin, her assistant Itoh, and the captured Mimiga escape on a helicopter, leaving the rest of the island's inhabitants to their fates.

Should Quote complete the aforementioned tasks, they may proceed into the Blood-Stained Sanctuary, a bonus stage where Curly can be found and rescued; it is also here where Ballos — creator of the Demon Crown and Jenka's younger brother — is imprisoned.

A powerful wizard who went insane and destroyed his homeland after being tortured by a jealous king, Ballos was sealed deep within the island by his sister.

[20] With the help of Curly Brace, Quote defeats Ballos and stops the source of the negative energy that was causing the island to fall, saving its inhabitants.

[24] Amaya admitted this lack of planning caused "problems down the line" because he did not have dedicated map editing and data management tools.

[25] While designing the main character, "Quote", Amaya drew inspiration from Mario's appearance, giving him a large, expressive face and a high contrast between his white skin and red pants that made him stand out from the dark cave backgrounds.

[25] To make levels memorable, Amaya designed them around a single theme, such as "warmth" for the Egg Corridor, and "arid and oppressive" for the Sand Zone.

[25] An enhanced port, featuring updated character designs, remixed music and extra game modes, was developed by Nicalis and released on WiiWare on 22 March 2010 in North America and 10 December 2010 in Europe.

The game was built from scratch using 3D character models, featuring a dynamic camera system and another additional level, as well as a remixed soundtrack by Danny Baranowsky.

[31][41][42] The Japanese version features crossover content from various NIS and other companies' franchises such as Crazy Climber, Ikki, and Dragon Slayer.

[43] In order to devote more time to perfecting the title, Amaya quit his job as a software developer to become director of Cave Story 3D.

[59] Matt Miller of Game Informer observed that it combines elements of Metroid, Ninja Gaiden, Mega Man, The Legend of Zelda, and Castlevania into an "engrossing, challenging, and quite lengthy" whole.

[64] The WiiWare version has received mostly positive reviews, with the central criticism being the 1200 Wii Point price tag (US$12, £10), after years of free play.

On the issue of price, he explained that "the prospect of Amaya finally earning a little something for the hard work he invested in this masterpiece strikes me as satisfyingly poetic" and "absolutely worth your money".

[50] John Teti of Eurogamer had similar sentiments, but also noted the technical issues with the remixed music, recommending the original soundtrack.

[53] Daemon Hatfield of IGN felt that Cave Story "belongs on a Nintendo system" and noted gameplay similarities to Blaster Master, in which damage reduces the power of weapons as well.

Many reviewers cautioned that the graphical update does not justify the $40 initial price point, especially with cheaper or free versions of the game available through download services.

[66] Audrey Drake of IGN noted that the 3D effect made it difficult to distinguish certain platforms between background and foreground, a complaint shared by Douglas.

[67] Simon Parkin of the UK Official Nintendo Magazine was more critical, citing lack of detail in the 3D models and a too-dark color palette.

[4] Despite the freeware nature of the game's initial release, official rereleases by Nicalis (since taking over its publishing for major platforms) have caused ambiguity regarding the usage of Cave Story's copyright and assets.

Further confusion has been caused by cease and desist letters as well as DMCA actions against fan projects using the game's assets as well as its decompiled codebase.