In the aftermath of Amagami SS, high school student Junichi Tachibana continues his relationships with the girls at his school. Amagami SS+ Plus offers a glimpse into what happened after the resolution of each girl's individual story. New events begin to take place between each of the girls and Junichi. Tsukasa Ayatsuji, the class representative, runs for student council president; Rihoko Sakurai, who has taken over the Tea Club with Junichi, still wants to confess her feelings to him; Ai Nanasaki questions the future of her relationship with Junichi when he leaves for college; Kaoru Tanamachi wonders if her relationship with Junichi will ever go any further; Sae Nakata and Junichi deal with classmates who still can't believe that someone so cute is his girlfriend; and Haruka Morishima wants to take their relationship to the next level and get married.

In class 3-3 of Yomiyama North Junior High, transfer student Kouichi Sakakibara makes his return after taking a sick leave for the first month of school. Among his new classmates, he is inexplicably drawn toward Mei Misaki—a reserved girl with an eyepatch whom he met in the hospital during his absence. But none of his classmates acknowledge her existence; they warn him not to acquaint himself with things that do not exist. Against their words of caution, Kouichi befriends Mei—soon learning of the sinister truth behind his friends' apprehension. The ominous rumors revolve around a former student of the class 3-3. However, no one will share the full details of the grim event with Kouichi. Engrossed in the curse that plagues his class, Kouichi sets out to discover its connection to his new friend. As a series of tragedies arise around them, it is now up to Kouichi, Mei, and their classmates to unravel the eerie mystery—but doing so will come at a hefty price.

Shortly before the start of a new semester, Misaki Fujioka visits her twin sister Mei Misaki in Yomiyama City. The girls make full use of the last days of summer, roaming around a heat-weary town and visiting various places including a shopping center and shooting stall. When they prowl around her basement, Mei expresses uneasiness about her new class, which is said to be cursed. Craving more entertainment, the twins decide to pay a visit to the local amusement park. But the leisure of a sleepy summer day could soon turn woeful as Mei sees the color of death on her sister—an unmistakable omen that a tragedy is bound to strike.

While testing out his camera on a bridge one summer night, Kaito Kirishima sees a blue light streaking across the sky, only to be blown off the railing seconds later. Just before succumbing to unconsciousness, a hand reaches down to grab ahold of his own. Dazed and confused, Kaito wakes up the next morning wondering how he ended up back in his own room with no apparent injuries or any recollection of the night before. As he proceeds with his normal school life, Kaito and his friends discuss what to do with his camera, finally deciding to make a film with it over their upcoming summer break. Noticing that Kaito has an interest in the new upperclassmen Ichika Takatsuki, his friend Tetsurou Ishigaki decides to invite her, as well as her friend Remon Yamano, to join them in their movie project. In what becomes one of the most entertaining and exciting summers of their lives, Kaito and his friends find that their time spent together is not just about creating a film, but something much more meaningful that will force them to confront their true feelings and each other.