IN Malus Code The user plays the role of Will, a scientist studying hot springs and thermophiles. He travels to Japan, where there are many hot springs and where he plans to get a job at a university. And there the protagonist meets several colleagues. Among them is a strange girl Yuri, who prefers to talk about herself in the third person, and Suzukake, the head of the laboratory, who has a mysterious connection with Yuri. Will joins their group, which leads to adventures that the researcher could not even imagine in his dreams.

In Malus Code, the plot is divided into three chapters. Unlike many visual novels, the storyline here is also completely linear. The user's choices affect only minor events. The main episodes and the ending remain unchanged. Otherwise, the gameplay is more traditional. The protagonist is able to interact with other characters, such as Yuri, and choose different options in dialogues. The gamer's choice determines the attitude of the characters and the outcome of secondary events.

The character sprites are made in the traditional anime style and their lines are fully voiced. The story itself combines several different genres. Among them, romance, adventure, and horror stand out. Another feature of the project is that many questions remain unanswered. Players are given only hints, from which they can try to assemble the full picture themselves.