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.

For high school students like Shouichi Kamita, university entrance exams and the future are common concerns. It is also during this time in life that a mysterious emotion that vexes people of all ages may begin to weigh upon one's mind—love. At this point in his teenage years, Shouichi finds three girls he could see himself having a future with: the ever-cheerful Hikari Tsuneki, who teases Shouichi without mercy, but actually has a softer side; the competitive gamer, Tooru Miyamae, who has difficulty communicating with others; and Shouichi's childhood friend, Kyouko Touno, the sometimes immature shoujo manga enthusiast. Seiren follows Shouichi's relationships with these three girls across three separate arcs, as their feelings grow from mutual interest and blossom into something more beautiful.

As his school days draw to an end, Yuuki Wakura worries about his future. While lamenting the prospect of living an ordinary life, he is suddenly drawn into the world of Mato: an alternate dimension filled with dangerous monsters called Shuuki. Over the years since the existence of Mato was first confirmed, incidents of people accidentally wandering into the other world have become commonplace. To combat the threat of the Shuuki and rescue victims like Yuuki, the all-female Demon Defense Force was established. Its members have been blessed with the power of Peaches—Mato fruits that grant supernatural abilities only to women. Though Yuuki's situation is dire, he is saved in the nick of time by Kyouka Uzen, the chief of the Demon Defense Force's seventh unit. Despite Kyouka's impeccable skills in battle, she has long been held back by her Peach-granted ability, Slave. Slave allows Kyouka to put a living being under her control and draw out its strength, but the Shuuki that she had enslaved until now had all proven to be exceedingly weak. When Yuuki and Kyouka become surrounded by a horde of Shuuki, Kyouka resorts to something she has never tried before: using her ability on a man. To her surprise, Yuuki's slave form is much more powerful than she could have imagined. Believing the young man to be the key to unlocking her true potential, Kyouka invites Yuuki to join the Demon Defense Force—but not as a regular member.

Once again, the Game Master's world of quests unexpectedly pulls in Yuusuke Yotsuya and the rest of this old team. Accompanied by the newest addition, Keita Torii, the team reunites with Kahabell, still unaware of their actions' impact on this world. After bidding Kahabell farewell, the team sets out on their newly appointed quest—an offering of a Jiffon Buffalo at Vaikdamnia on Jiffon Island. However, as their journey to the island commences, the team shortly finds that the quest is not as simple as it initially seemed. In fact, the island is terrorized by orcs that have made a deal with its inhabitants: instead of devouring the islanders, the orcs will be granted buffalo. With the growing shortage of buffalo, the annual Vaikdamnia festival cannot proceed. But, given the importance of the team's quest, they are left with the obvious choice—rid the island of the orcs and save the islanders.