"Your innermost desires determine your real purpose."
In Koukaku no Pandora, two young cyborgs cross paths on a cruise heading towards the stunning Cenacle Island—a popular tropical destination that not only offers world-class vacation luxuries, stunning scenery and services, but also cutting-edge technology. During their short voyage, the two are somehow able to create an unconventional friendship. However, their fateful bond is soon threatened when an unexpected explosion, upon arrival, brings about chaos on the island.
Nene Nanakorobi, a young and bubbly cyborg who wants nothing but universal peace, tries to overcome her fears to find her new friend, Clarion. Postponing her initial plan to visit the island, she courageously faces her limitations and weaknesses in order to save her buddy because that's what friends are for. Can Nene and Clarion find their way to each other again? Will they be able to stop (or even find) the bringer of disorder? Or will they be destroyed in the process?