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Tear Jerker: Tantei Gakuen Q
The case that involved Shino and the murder of her Unlucky Childhood Friend, as well as the one featuring Kyuu's childhood friend Kaoru and her Big Screwed-Up Family, Sympathetic Murderer Miyo Fuuma's heartbreakingVillainous Breakdown, the scene where Kuniko reveals herself as the victim of brutal online bullying... to the guy she used to love, and who killed someone else believing that he had driven his e-girlfriend to kill herself., and also when Ryu Takes the Bullet in Kyu's place during the case of the violinist Mitsuru Hoshou, specially after seeing him struggle hard with himself before.
There's also the case where the victim is Shino's Unlucky Childhood Friend Tojukou. Megu was upset because of Shino's apparent unsensitivity to this and storms off, but Kyuu convinced her to return. When they returned to the crime scene, they saw Shino covering Tojukou's lifeless body with a sheet and taking care of him, which drives Megu to tears.
Megu: " Katagiri-sensei... I'm sorry! I'm so sorry!"