Through their tutor Fuutarou Uesugi's diligent guidance, the Nakano quintuplets' academic performance shows signs of improvement, even if their path to graduation is still rocky. However, as they continue to cause various situations that delay any actual tutoring, Fuutarou becomes increasingly involved with their personal lives, further complicating their relationship with each other. On another note, Fuutarou slowly begins to realize the existence of a possible connection between him and the past he believes to have shared with one of the five girls. With everyone's feelings beginning to develop and overlap, will they be able to keep their bond strictly to that of a teacher and his students—or will it mature into something else entirely?

Fuutarou Uesugi's efforts as the Nakano quintuplets' private tutor are finally paying off. The academic performances of the five sisters are steadily improving, and they are each closer than ever to achieving their respective dreams. However, it appears that Fuutarou has become more than a teacher for the girls, who urge him to sort out his feelings. The undecided young man promises to make a decision by the end of the school festival. However, Fuutarou's task will not be easy, as the Nakano sisters pull out all the stops to win his heart before it is too late.

Fuutarou Uesugi is an ace high school student, but leads an otherwise tough life. His standoffish personality and reclusive nature have left him friendless, and his father is debt-ridden, forcing his family to scrape by. One day during his lunch break, Uesugi argues with a female transfer student who has claimed his seat, leading both of them to dislike each other. That same day, he is presented with a golden opportunity to clear his family's debt: a private tutoring gig for a wealthy family's daughter, with a wage of five times the market price. He accepts the proposal, but is horrified to discover that the client, Itsuki Nakano, is the girl he confronted earlier! After unsuccessfully trying to get back on Itsuki's good side, Uesugi finds out that his problems don't end there: Itsuki is actually a quintuplet, so in addition to her, he must also tutor her sisters—Miku, Yotsuba, Nino, and Ichika—who, despite the very real threat of flunking, want nothing to do with a tutor. However, his family's livelihood is on the line so Uesugi pushes on, adamant in his resolve to rid the sisters of their detest for studying and successfully lead them to graduation.

Iori Kitahara moves to the coastal town of Izu for his freshman year at its university, taking residence above Grand Blue, his uncle's scuba diving shop. Iori has high hopes and dreams about having the ideal college experience, but when he enters the shop he is sucked into the alcoholic activities of the carefree members of the Diving Club who frequent the place. Persuaded by upperclassmen Shinji Tokita and Ryuujirou Kotobuki, Iori reluctantly joins their bizarre party. His cousin Chisa Kotegawa later walks in and catches him in the act, earning Iori her utter disdain. Based on Kenji Inoue and Kimitake Yoshioka's popular comedy manga, Grand Blue follows Iori's misadventures with his eccentric new friends as he strives to realize his ideal college dream, while also learning how to scuba dive.