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This episode (episode 76 of ADV "Me, Myself and Time") is such a weird one. A girl travels back in time to get her younger self's help in research on an ancient Baltoy civilization. Ash gets involved because he gets lost in the fog, and Team Rocket shows up because they're contractually obligated to.
It almost feels like a prototype of what we'd later get with Twilight Wings and PokeToons, Just a story in the Pokemon world completely estranged from the ongoings of the Ashnime. I really kept wondering during the episode why Ash needed to be here, and why this couldn't be a Generations special.