Nazo no Murasme-jō takes place in the Edo period Japan. One stormy night, the grand Murasame Castle is attacked by aliens, and a giant statue known as Murasame comes alive. The alien used their power to take control of four nearby castles and their four daimyo using four powerful orbs. The leaders then use the orbs to summon ninja and other evil creatures that attack the people in the land. To protect the land, the shogun sends Takamaru on a mission to infiltrate the castle and bring peace back to the land.
Takamaru traveled through the land and the four castles, killing the four daimyo and destroying the orbs on his way. He also rescued the daughters of the daimyo in the castles before he finally reached the Murasame Castle. After making his way through the by now totally twisted castle, Takamaru challenged the Murasame Statue. Destroying it revealed a path to the aliens' world where he once for all destroyed the alien.
Captain Rainbow: Takamaru finally returned in Captain Rainbow as one of many "forgotten Nintendo characters". He had come to Mimin Island wishing to learn to control his excitement around women.
WarioWare D.I.Y.: In the Japanese version of the game there is a micro game based on Nazo no Murasame-jō, in which the player needs to make Takamaru invisible to avoid enemy attacks.
Samurai Warriors 3: Takamaru appears as a playable character in a special mode based on Nazo no Murasme-jō. After gather 33 Tanuki statues, Takamaru becomes playble in Free Mode.
Nintendo Land: Takamaru will offer his name to a mini-game of this Wii U game, where the player will be able to throw shurikens at other ninjas with the Wii U GamePad
Super Smash Bros. for Nintendo 3DS / Wii U: Takamaru appears as an Assist Trophy. He had at one point in time been considered as being a playable character, however Sakurai felt that due to his low popularity in the west, it was best he be downgraded to Assist Trophy status.