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Tear Jerker: B't X
The mines underneath the Empire's tower are running out of oxygen and Kotaro is trying to figure out how to kill Raphaello. Marcello breaks down crying because he can't even look at the sun before he dies. Kotaro does what he can and writes out the formula for sunlight, before he starts crying too because that's how little he can do to save a life despite being a scientist.
Alternatively, in the anime Amigo's You Shall Not Pass, strapping himself to the door just to keep Kotaro safe also qualifies.
The dead of Kaos and his BT, made more heartwrenching when Kaos can finally die happy knowing Teppei will surely triumph.