Moyashimon Moyashimon Returns

Professor Itsuki divides the students into two groups for the creation of different fermentation products. Oikawa discovers a secret entrance which is later no longer there. She begins to suspect that the others are hiding something from her.

Tadayasu teams up with Oikawa to find the truth about the mysterious door while Haruka is warned by her father that the time is running out for her to wrap up her research and fulfill the promise she made to him.

Haruka is worried about her father's demands while Tadayasu and the others pay a visit to the remodeled Hiyoshi's liquor store and learn about what lies behind the secret door. Oikawa gets depressed about not finding anything important after so much effort to discover about it, and to cheer her up, Tadayasu decides to reveal his secret to her.

Tadayasu confesses his secret to Oikawa, but she does not believe him at all. Haruka is picked up by her father who leaves her letter of resignation in Mutō's hands. While Haruka embarks on a trip with her fiancé against her will, the students start to make preparations for the upcoming Harvest Festival. Oikawa and Mutō refrain from telling the boys the truth about Haruka's sudden abscence.

The Harvest Festival begins. Misato and Kawahama mount a Tequila stand resorting to suspicious tactics in their scheme to win the Grand Prize, while leaving Tadayasu and the others to attend the customers by themselves. Meanwhile, Professor Itsuki makes his move in an attempt to bring Haruka back to the University.

As the Harvest Festival goes on, Tadayasu learns the reason for Haruka's abscence, while her father falls in Professor Itsuki's trap. Misato and Kawahama's grand scheme is a success, but instead of keeping the money they decide to buy plane tickets for Mutō and Tadayasu to look for Haruka in France.

Misato and Kawahama's antics during the Harvest Festival cost them a 20 days suspension and Professor Itsuki takes the oportunity to have them accompanny Tadayasu's search for Haruka in Paris. Despite Sawaki's protests, the trio ends up goofing arround the city until all their money runs out, and only then they finally start to look for her. Little they know she is already far away from the capital, in the outskirts of Mont Saint-Michel.

While looking for Haruka in Burgundy, Sawaki and co. stumble on Marie, a French girl who also speaks Japanese and has a striking resemblance with Yuuki. The trio is drafted by Marie to work as waiters in a special banquet held at her place, and much to their surprise, they finally meet Haruka in the occasion.

Haruka asks for Misato and Kawahama to take her back to Japan, but with her fiancéé's escorts looking for her, they decide to go separate ways to evade them. Sawaki confronts Marie about her relutance to inherit her family's winery despite she is so enthusiastic about her life on it, while Misato and Haruka manage to evade her pursuers and surprisingly end up having some quality time together.

Sawaki and the others bid farewell to Marie, but before departing, Sawaki have the microbes there to write a message of encouragement to her and her father. Haruka returns to confront her fiancéé just to find him ill. As she tends to his condition, the two finally comes to terms.

Before returning home, Sawaki and his friends meet Marie once more and learn that the messages left by the microbes helped her family to resolve their differences and move on with their family business. Finally back at Japan, Hasegawa wonders about what she should do from then on, as with her engagement cancelled, there is no reason for her to remain at the university, but Sawaki encourages her to move on with her carreer not for obligation but for doing what she really wants to.