I don't see how that can count, really. It did look remarkably like other depictions of thunder being used, but that's it. At that point Pikachu hadn't even learned thunderbolt yet, which comes way before thunder in the order its moves are learned. And you have to remember that as early on as that they seem to have been adhering more strictly to game mechanics as they pertain to levels and such.

Furthermore, there was already a thunderstorm raging at that point, which is where Pikachu drew most of the energy from, not itself. I wouldn't consider that as Pikachu knowing thunder any more than I would say Pikachu defeated Takeshi's Iwark using its own power. If it had really known the move thunder then it could have used such power by itself all along, which it didn't until episode 42.

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