Negaeba Kitto tells the story of a young man who has recently been treated for a serious illness, and who finds a certain kind of redemption in the most unlikely place.
The game is the first sequel to Navel's first game, Shuffle!, continuing Nerine's path.
The basic set-up is that Rin, Nerine, Itsuki, and Mayumi find a strange watch that transports them back in time, where they met Forbesii before he is married and has Nerine. While he is engaged to Ai, his maid, Sage, is also in love with him, causing a love triangle. The players actions determine who Forbesii ultimately ends up with, and thus who is the mother of Nerine.
For reasons completely unknown, Chisato Mikogami kills herself. She comes back as a ghost and wanders the earth, meeting the many interesting spirits and ghosts that make up the afterlife. Like Fishman, a fish spirit with a grudge against Chisato; Chisato's crazy sister who experiments on her, Chiyu; and their insanely powerful Mom.
Jun is an average student who lives with his mother. During winter holidays his childhood friend Kaede Sakurai helped him with his homework. By that time Jun realized his feelings for Kaede and due to some misunderstandings their ways separated.