A continuation of the epic adventure of plucky Riko and Reg who are joined by their new friend Nanachi. Together they descend into the Abyss' treacherous fifth layer, the Sea of Corpses, and encounter the mysterious Bondrewd, a legendary White Whistle whose shadow looms over Nanachi's troubled past. Bondrewd is ingratiatingly hospitable, but the brave adventurers know things are not always as they seem in the enigmatic Abyss.
After Noboru saves Hayase from drowning by giving him mouth-to-mouth, Hayase grows confused about his feelings. It doesn't help that around the same time he meets Noboru's twin brother, Ryū, who has a very different, outgoing personality.
The Metropolitan Police Department '0'section, known as an organization in the police department that investigates a closed case. Well-trained detective in the '0' section, Ray, is looking for her memory that was lost during the training, while also investigating a human traffic which young woman being a victim. One day, classified killer virus was seized by rising terrorists. To investigate this case, public safety sent Sarah Kodama who specializes in molecular biology and computer, to work with Ray but Ray refuses to work with Sarah. Sarah was curious about mysterious Ray, she starts to collect Ray's information and goes to see Ray's former boss, Asami. However, the man who appeared in front of Sarah was an assassinator who contemplates destruction of '0' section. What happens to Sarah...!? What is in Ray's lost memories!?
Bonobono: Kumomo no Ki no Koto was the second theatrical Bonobono movie, released by Amuse Pictures in theaters in Japan on August 10, 2002. It was done completely in 3D.
