I'd forgotten how much heavy lifting Flooded does in setting up the rest of S6. You've got Buffy hanging on by her last emotional thread, Willow's deep-rooted insecurity rapidly becoming dangerous instead of cute, introduction of The Trio...it's a lot for an ep I mostly remember for No! More! Full! Copper! Repipe!
(This is also the ep when Angel finds out Buffy is alive again and they reconnect offscreen between episodes, and so one of the few times in the seasons when watching in broadcast order would have made more sense, but oh well.)