Under Nariyuki Yuiga's devoted tutelage, his classmates Rizu Ogata, Fumino Furuhashi, and Uruka Takemoto are finally pulling average test scores on their worst subjects. But time is ticking, and there is still a long way to go before the three geniuses of Ichinose Academy are ready for their upcoming university exams. Meanwhile, the girls still struggle to balance the pursuit of their dreams with their growing affections for their unsuspecting tutor. Joining them are Mafuyu Kirisu, a teacher with strong views about education and talent because of her past as a rising figure skater, and Asumi Kominami, a graduate from their school aiming to attend a national medical university. With these two additions, the group of six is livelier than ever before. Completely caught up in hilarious antics with his new friends, Yuiga finds that his last year of high school now includes a lot more than just going to class and studying.

For Hikari Tsutsui, life within the two-dimensional realm is much simpler. Socially inept and awkward, he immerses himself in video games and anime, only to be relentlessly ridiculed and ostracized by his classmates. Sharing his misery is Yuuto Itou, his only friend, who wears cat ears and is equally obsessed with the world of games. After being forced to clean the pool as punishment for arriving late, Tsutsui meets Iroha Igarashi, but he attempts to steer clear of her, as her notoriety precedes her. Brazenly blunt, loathed by female classmates, and infamous for messing around with boys, Tsutsui believes that getting involved with her would cause nothing but problems. 3D Kanojo: Real Girl is a story revolving around these two outcasts—a boy full of emotions he has never experienced before, struggling to lay them bare, and a girl who strives to break him out of his shell.

Rentarou Aijou has it all: looks, intelligence, athletic skill, and popularity with peers and mentors alike. Unfortunately, none of these qualities help Rentarou with his love life. On the day of his middle school graduation, he is once again turned down by a girl he confesses to, earning his one-hundredth rejection in a row. Down on his luck, he goes to a matchmaking shrine and wishes to finally get a girlfriend in high school. When the god of the shrine suddenly appears before him, Rentarou is told he will meet an astronomical total of one hundred soulmates in high school. Though Rentarou initially does not take this foretelling seriously, his doubts disappear when, on the first day of school, he meets two of these soulmates—Hakari Hanazono and Karane Inda—who both confess to him. With fated encounters and love confessions galore, Rentarou's life is about to get a lot more exciting.

On a rainy day, Ryou Fujibayashi musters up the courage to confess her feelings to Tomoya Okazaki. Despite not knowing each other for long, the two start dating and develop a harmonious relationship. However, tensions begin to rise when a rumor surrounding Tomoya and Ryou's older sister Kyou spreads around school. Navigating through a web of emotions, Tomoya and the Fujibayashi twins determine where their love truly lies—even if it means standing in the downpour of the heartbreaking truth.