После взрыва во время Токийского саммита на сайте появляется тень Тору Амуро, сотрудника Бюро безопасности национального полицейского управления, также известного как Зеро. Также появляется трехликий Рэй Фуруя, известный как детектив и ученик Когоро Мори, но являющийся членом Черного синдиката по имени Бурбон. В результате всех этих событий Когоро ареставан по подозрению в причастности к взрыву. Конан начинает расследование, чтобы доказать невиновность Когоро. Какую роль в расследовании сыграет Амуро?
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?
