The Pokemon had the pokerus virus and recovered from it.
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Don't you mean yellow not lighting yellow? Anyways you get charmander past Nugget Bridge and off to the left and a guy gives you it.
Do you maybe mean WHITE? Cuz yeah, it's a LOT different from Yellow, by about 4 generations...
It means that that certain Pokemon had pokerus and is no longer able to get pokerus again
On the pokemon's info screen? That means that your pokemon has recovered from Pokerus. All it means is that the pokemon will now gather EVs at twice the usual rate.
To my knowledge i don't think there is a waterfall in Pokemon yellow and it is quite irrelevant to the storline if there was one. If you mean a HM named waterfall...i think your on the wrong game, only pearl and diamond have waterfall HM...i think. There are only 5 HM's in Pokemon Yellow Flash, Cut, Fly, Surf, Strength.