Als der Student Cacao eines morgens aufwacht, liegt ein grünhaariges Mädchen neben ihm in seinem Bett. Leider können weder er noch Hinano sich erinnern, wie es dazu gekommen ist. Also beginnt Cacao an seiner Universität, der Micro-Grand-Universität, nachzuforschen, was am Tag zuvor passiert ist. Dabei stößt er auf Professor Ganache, dem Professor für Magie an der Mirco-Grand-Universität. Dieser kann Cacao auch erklären, warum Hinano aus »Holz« besteht.

Cacao, étudiant à la Micro Grand Academy, une école de magie, se réveille un matin et trouve une fille dans son lit. À un détail près : celle-ci s'appelle Hisano et n'est autre que l'esprit d'un arbre que possédait une marionnette en bois que Cacao a manipulé en cours. Étrangement attirée par Cacao, Hisano décide de s'inscrire dans son école...

Trouble Chocolate is a comedy anime produced by AIC in 1999 and is licensed in the United States by Viz Media. The series features Cacao, a student at Micro-Grand Academy studying magic. One day, while his magic class teacher, Ghana, is performing a spell to summon a tree spirit, Cacao finds and eats some chocolate, which turns out to be 200 year old magical chocolate. After eating the chocolate he becomes drunk and causes a wreck. During this, he interferes with Ghana's spell, letting the spirit, Hinano, escape. She inhabits the body of a marionette, who then moves in with Cacao.

Subsequent episodes of Trouble Chocolate have little connected storyline. Rather, the show is a parody of other anime. For example, two other characters, Murakata and Deborah, are constantly shown professing their love to each other, set to absurdly explosive special effects and backdrops, as is common in many anime.

The dubbed dialogue in Trouble Chocolate often bears little or no resemblance to the original script, as opposed to the normal convention of translating the words as directly as the change in lip-sync will allow.

クランキー堺町のマイクログランド学園を舞台にした、世紀末＜おバカ＞ドタバタドラマ。マイクログランド学園は職員・生徒あわせて１０万人。クラブ同好会もベーシックなものから奇妙奇天烈なものまであわせて１６００部会という‥‥まさにマンモス高校（死語？）しかしここの生徒・先生、ただ頭数が多いだけじゃない。なくて七癖、味の濃ぉ～いキャラクターばかり。質量共にヘビー級のこの学園、今日もトラブルが絶えません。さて今週はどんなはちゃめちゃが起きるやら‥‥

Cacau acordou e encontrou uma garota dormindo ao lado dele. Incapaz de se lembrar do que havia acontecido por conta própria e não recebeu as respostas necessárias de Hinano, ele foi à escola perguntar aos amigos o que havia acontecido. Ele finalmente conseguiu a explicação. de eventos do Prof. Gana, no termo cacau, ingressou em sua aula de magia.