The film tells the story of a new transfer student interested in her surroundings, and a song that brings happiness to her and her classmates.

After the defeat of Myouri Unzen at the hands of Medaka Kurokami and her Student Council, peace has returned to Hakoniwa Academy—at least, for a short while. Soon, Medaka, Zenkichi Hitoyoshi, Kouki Akune, and Mogana Kikaijima find themselves wrapped up in another sinister scheme, known as the "Flask Plan," led by the school's principal himself. However, the council's first problem is to deal with a whole new group of superhuman students calling themselves the "Thirteen Party," led by the egotistical but powerful Oudo Miyakonojou. With the mysterious Flask Plan, Oudo's tyranny, and the resurfacing of an old enemy, the state of Hakoniwa Academy is far from tranquil, and Medaka and her companions have their hands full as things only get a lot more abnormal. [Written by MAL Rewrite]

Medaka Kurokami is, in the truest sense of the word, perfect. Beautiful, intelligent, and athletic, Medaka's dream is to make others happy. So when she runs for Student Council President of the prestigious Hakoniwa Academy, winning the election with 98% of the votes is only to be expected. The very first thing the boisterous new president does is set up the "Medaka Box," a suggestion box allowing students to submit any kind of request for assistance. Together with the cynical Zenkichi Hitoyoshi, her childhood friend who has been strong-armed into helping, Medaka fulfills these requests at a ridiculous rate. For every job completed, she adds flowers to the student council room, with the aim of filling the entire school. However, the two are about to find out that helping others may be a lot harder than they think as they begin to uncover a devastating plan centering on the academy and even Medaka herself! [Written by MAL Rewrite]

Yuugo Hachiken is studious, hard-working, and tired of trying to live up to expectations he just cannot meet. With the ushering in of a brand new school year, he decides to enrol in Ooezo Agricultural High School, a boarding school located in the Hokkaido countryside, as a means to escape from the stress brought upon by his parents. Initially convinced that he would do well at this institution, Hachiken is quickly proven wrong by his talented classmates, individuals who have been living on farms their entire lives and know just about everything when it comes to food, vegetables, and even the physiology of livestock! Whether it be waking up at five in the morning for strenuous labor or to take care of farm animals, Hachiken is a complete amateur when it comes to the harsh agricultural life. Gin no Saji follows the comedic story of a young student as he tries to fit into a completely new environment, meeting many unique people along the way. As he struggles to appreciate his surroundings, Hachiken hopes to discover his dreams, so that he may lead a fulfilling life on his own terms. [Written by MAL Rewrite]