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Tear Jerker: Flint The Time Detective
Flint The Time Detective gives us Artie, whose bond with a young Auguste Rodin was incredibly close, and who clings, sobbing, to Auguste when the time comes for Flint and co. to take him away forever. The boy promises to never forget him...before having his memories forcefully wiped clean. For the remainder of that episode, Artie never stops crying. Honestly, it's like seeing Pikachu taken away from Ash with a little Mind Rape thrown in for good measure.
In fact, whenever Time Shifters befriend various figures throughout history, it's a given that they'll get no happy ending.