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So in S/M, after the Rocket castle fight, but before you went off to go save Lillie's mom, am I mistaken in remembering that the PC and Lillie slept in that same bed together? She also started acting more confidently after that, so my headcanon is that the PC gave Lillie a backbone through the power of the D.
(And she left the islands to go raise the kid she was having if you played the male PC)