Unlike the three previous films, Pure focuses on the relationship between Misu Arata and Shingyouji Kanemitsu , which begins when Shingyouji takes the test to enter Shidou Gakuen . That's when he meets Misu and falls for him. Then we come back to the present where the sempai who admires Misu appears, bringing Shingyouji problems and jealousy.

It's June of their third year of high school, and Takumi has an important anniversary to attend back in his hometown. He wants to invite Gii along for the trip, but time and scheduling and possibly broken promises stand in the way.

The story takes place at Shido Academy, a boarding school for boys, and centers on Hayama Takumi, a lonely and shy boy who suffers from an extreme phobia of human contact and can't stand being touched by others. During his second year of study, Takumi has to share his room with Saki "Gui" Giichi. Gui was raised overseas and is the school idol due to his outstanding academic performance and good looks. One day, Gui confesses to Takumi that he has been in love with him for some time. This truth unsettles Takumi, but however, he comes to realize the true sensitivity of Gui's personality.

Takumi and Gii are now a couple, but Takumi is still uncomfortable with showing affection. Not only that, but Takumi grows jealous when Gii starts paying attention to a good-looking first year student. Is Gii's love really that fickle?

Another school year is starting. Upon meeting up with Gii, Takumi is worried when it turns out Gii has changed, suddenly acting cold and distant. Could their relationship be in danger for real this time?

A 2nd year student is assigned a handsome new roommate at the start of the school year.