After a sudden explosion at Edge of Ocean island in Tokyo, Tōru Amuro, codename Zero, begins to investigate. Meanwhile, private eye Kogorō is arrested as a suspect, so Conan Edogawa conducts his own investigation to prove his innocence, but Amuro stands in his way.
The special takes place during the two year before the Straw Hats reunite on Sabody. Luffy is currently in Rusukaina training to get stronger to take on the New World. However the training is interrupted when Hancock's sisters, Marigold and Sandersonia, are kidnapped by the Byrnndi World, a pirate who was locked away on Level 6 of Impel Down but escaped during Luffy's invasion to save Ace, in order to lure Hancock to him and use her as a hostage against the World Government due to her Shichibukai status. Thus Luffy and Hancock head off to confront him and save Hancock's sisters.
Kobayashi Manabu's new life as a freshman at the prestigious Kirameki High School begins. As he explores the new school with a video camera, pretending to collect data as a member of the student council, he conducts several interviews with the female heroines of the story.
Gifted thief Lupin the Third scores a "magic lamp" and finds it contains a genie. However, after the clock strikes 7 p.m., he can't seem to remember anything… Finding himself in Singapore, Lupin must battle his way past the forces of Colonel Garlic and discover the secret behind the lamp – but every night at 7 p.m., his memory is wiped clean! How can Lupin piece together this puzzle when he can't even remember what he's doing?