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The flashback that shows how Yggdrasil and Pronyma first met.
The end of Unreal Society, doubling as a tear jerker. The world exists. Everything did have a purpose. Ichigo and Sheena's reunion at the very end, in great homage to the Good Ending in the sequel is the cake toper of this moment
In chapter 12 Ichigo says to Kratos that he has no idea how he'll prove that Ratatosk won't destroy the world only to add that Lloyd really had no idea what he was doing when he did his journey either. It's because this is Ichigo that we're talking about and how nice of a tie in it is to the first game/fic that its a good example.
In the sequel when Ichigo and Sheena reunite.
Chapter 19 of Return of the Samurai when Sheena starts having all her flashbacks.
In Return of the Samurai, after Lloyd finally joins the group Colette says to him Welcome Back.