It’s been two years since the end of the Fourth Great Ninja War. Shikamaru now has an important role within the Hidden Leaf government, and as a representative of the Leaf in the Alliance. One day, a situation develops with shinobi disappearing in droves, and Shikamaru takes on a dangerous mission.

Conan suddenly wakes up in the darkness. While walking with the Detective Boys to go shopping, Conan witnessed a figure breaking open a safe inside a building. Conan was attacked by the culprit and imprisoned inside a rectangular box. Meanwhile, Kogoro is hired to find the thief who stole the will of Karabashi Group chairman Karabashi Gotaro. The suspects have been narrowed down to Kozo the eldest son, Mitsuyo the eldest daughter, and Hideo the second son. Conan manages to get in touch with the Detective Boys using his badge, but he soons finds himself cornered in a desperate situation...

K is attempting to open another monster gate. To prevent K's plans from succeeding, the gang heads to a physics research facility. Taiyo and Shino join up in search of clues.

After discovering K's ambitions, Ren and the rest of the gang return to Kaminohara. Telling Haruma that he wants to check on something, Akira heads to the hospital where Haruma's mother lies in a coma.

It becomes apparent that the one who sent Memento Mori was none other than K, who reveals himself to be Genma, Haruma's father. Why did the Warrior Gods appear? What is their connection to the happenings in Kaminohara? Genma reveals his ambitions...

Shino, Mariko, and Kaoru rise against Memento Mori to rescue Haruma. Romeo, Alice, and Himiko's bump combos push back Memento Mori. However, in the field appears a black coffin...

Memento Mori, the Spirit of War, shows herself to be the cause behind Haruma's pain. Ryoma holds the elemental advantage, fire against wood. As Ryoma moves in to finish the battle in one blow, a fog obstructs his path...