The story follows Goemon's struggles to prevent the Peach Mountain Shoguns gang from turning Japan into a Westernized fine arts theater.

The plot calls for three cinematic musical features and battles between giant robots; like other Ganbare Goemon games, it is peppered with surrealist humor and anachronisms.

[3] Reviewers praised its graphics, gameplay, and humorous plot, while criticizing its virtual camera and questioning how accessible its references and jokes would be to Western audiences.

Goemon and his friends can walk or run, jump, attack, and use special abilities to cross terrain, pick up money, and defeat enemies.

These sequences begin with a music video and a high-speed minigame in which Impact must smash structures and avoid hazards while racing across the countryside.

Impact can punch, kick, defend, reel in opponents with the chain pipe, and use projectile weaponry, including nasal bullets and a laser.

[6] Collecting all the fortune cats and beating the game enables an Impact tournament mode with a special image of the robots as the prize for winning.

[6] Goemon lives in Oedo Town and is friends with Ebisumaru, a strange, gluttonous fat man who wears a blue bandana.

[6] Their kunai-throwing friend Sasuke is a mechanical ninja (made by the Wise Man of Iga) who enjoys hot baths and Japanese tea.

[6] The villains of the game hail from the organization Peach Mountain Shoguns and include a gang of four "weirdos" led by Spring Breeze Dancin' (Danshin Harukaze) and Kitty Lily (Margaret Ranko).

While shopping in Oedo Town, Goemon and Ebisumaru feel the ground quake as a peach-shaped flying object sails overhead.

In Zazen Town, Goemon finds Yae, who claims the troublemakers responsible are Flake Gang members named the Peach Mountain Shoguns.

[11] Goemon accepts the unconscious, powerless Sasuke and walks to Kii-Awaji island, where the dragon-powered passenger ferry has been stopped by the dragon's sudden craze.

They destroy a guard robot, prompting Gang of Four member Sharon to appear with Kitty Lily, the second leader of the Peach Mountain Shoguns.

The witch summons Wise Man, who tells Goemon to gather the fourth miracle items at the Stone Circle near Festival Village for passage into outer space and Kyushu.

After sidestepping grills and swimming through gallons of soup, Goemon confronts Poron, the final weirdo, who jokes that he lost the last miracle item in Zazen Town.

The son sits on a precipice inaccessible save through jumping training; Sasuke volunteers in the Chu-goku Region and acquires the miracle item.

Goemon locates Omitsu and learns that Dancin' and Lily can be found past a rigid gate, accessible only with the help of Wise Man.

Goemon summons Impact to fly into outer space, where he thwarts the giant peach ship Balberra and duels Lily and Dancin' in their personal battle robot.

The Japanese producers wished to break the series' numerical naming pattern to stress that Mystical Ninja differed from its forefathers.

[21] Konami targeted children, among whom the series is popular in Japan, by scheduling appearances of a Goemon mascot at some elementary school gymnastics sessions.

[30][31][32] Mystical Ninja featured a cartridge size of 128 megabits, designed to be much larger than most of its peers and predecessor games to allow high quality musical numbers and voice samples.

The soundtrack was later extracted from Read-only memory and presented in Nintendo Ultra 64 Sound Format on May 9, 2005; it is one of the most downloaded releases at USF Central.

[39] GameSpot said that though Mystical Ninja Starring Goemon borrows heavily from Super Mario 64, its gameplay is more varied and, due to it having the most memory of any Nintendo 64 cartridge to date, it has a much wider variety of textures.

Nintendo Power said the translation is poor and the story nonsensical,[49] GamePro found the untranslated battle cries to be alienating to U.S. gamers,[50] and a critic for The Tampa Tribune wrote, "attempts at humor often come across as rather inane.

[51] GameSpot and IGN maintained that the localization is exemplary, and that the content of the game is simply too specifically Japanese to be relatable or even understandable to the average non-Japanese gamer.

[47] GamePro said the game "never gets anywhere near exciting" and has a bland story, but succeeds well enough on the platforming front to make an acceptable holdover for RPG enthusiasts who could not wait for The Legend of Zelda: Ocarina of Time.

"[57] A reviewer for the Sentinel & Enterprise wrote in 2001 that while considered a "flawed 3D platformer", Mystical Ninja offered "quirky" fun "following the heels of Super Mario 64" by inviting players to "scale mountains, invade pagodas, and pilot giant robots in all-out fisticuffs to the rhythm of Japanese lyrics and pop tunes.

Featuring gameplay similar to the Super Famicom entry Ganbare Goemon 3: Shishijūrokubē no Karakuri Manji Gatame, the game presented a story in which Yae had been kidnapped by the Black Ship Gang.

[64] After a series of sequels on the PlayStation line of consoles, Konami returned to the medieval, quirky Japanese themes of Mystical Ninja and its brethren on June 23, 2005 with Ganbare Goemon: Tōkai Dōchū Ōedo Tengu ri Kaeshi no Maki for the Nintendo DS.