Directly following the prequel, Carpe Diem Reboot continues the story of Ai, an artificial intelligence program, and Jung, its programmer. As the programmer, Jung is faced with ethical and moral questions of how to treat what used to be just a computer program. As the program, Ai, who has achieved sentience, has begun to question her existence, and whether she can consider herself alive. The story introduces a new character, Yume, a technophile and a big fan of Jung and the organization he is involved with.

Which life path will Jung take? Will an advanced intelligent being like Ai be considered as human? Does Yume have the right to interfere with the decisions Jung make towards his own creation?