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Tear Jerker: Fractale
Clain witnessing what happens to the Phryne clones that have been deemed "useless."
The ending of the episode. Especially when Phryne's clone holds onto the cloth Clain bandaged on her wounded hand and smiles at him right before the temple underground base explodes.
Episode 10: While Barrot fondles Phryne, the ending scene cuts to Phryne still holding Nessa's hand.
Episode 11: The recording of the original Phryne. By itself it's not anything special, but coupled with Barrot's revelations earlier in the episode it heads straight for this. Also, there is the subtle implication that her father was the one that raped her.