Adult Fear: When Conan was kidnapped by Vermouth and everyone panics. Those who know the kidnapper have even more reason to fear because the Black Organization has no problem indoctrinating young children into complete loyalty to the organization. Jodie has a brief vision of an older, ruthless Conan preparing to kill a victim and is appropriately horrified.
Adults Are Useless: Averted, except in the case of Kogoro. Eri Kisaki, Yuusako and Yukiko Kudo, Heizo Hattori, Ginzo Nakamori, the police, and the FBI are all quite competent.
Busman's Holiday: Carries over from the series. Constantly Lampshaded. In the Omake, ten years after the fall of the Organization and Shinichi's return to full size, the "curse" seems to have lifted.
Canon Welding: It’s a Crossover fic between Detective Conan and Magic Kaito, but takes it even further than Conan itself has gone: Not just Kaito, Nakamori, and Hakuba show up, but just about everyone else from MK does too. Aoko, Akako, Snake (also code-named Sake, he’s part of the Organization,) Jii, Chikage, and in a couple of flashbacks, Aoko’s (dead) mother.
Cameo: Inspector Zenigata shows up for a cup of coffee with Inspector Nakamori. Also, some of the author’s friends make recurring cameos, including the suspects (and victim) in the first murder.
Cherry Blossoms: They remind Heiji of his first love, Kazuha, as seen in Movie 7.
Clothes Make the Superman: A variant, carried over from the original: Conan/Shinichi’s mind is as sharp as it ever was, but in the body of a kid, he’s no match for an adult, hence his gadgets.
Drives Like Crazy: Yukiko and Sato. Comes in handy at least once each. Early on, Yukiko brings Heiji to the train station fast enough that he’s not late picking someone up. On a more serious note, she manages to get Shinichi back to their house before he shrinks. And Sato saves her life and the life of Takagi after the brakes were cut and the acceleration sabotaged.
Early-Bird Cameo: The aforementioned friends of the author show up at a Karaoke place before being involved with a murder.
Enemy Mine: Everyone ends up working together to bring down the Organization, including multiple amateur detectives, the police, the FBI, and the Kaito KID. Inspector Nakamori and Saguru Hakuba both say at least once that they’d rather catch the BO than the KID.