In most of Johto and Kanto in Pokemon Crystal, whirlpools naturally occur in the water. No one Pokemon is responsible for the general amount of whilpools in Pokemon Crystal, and they simply serve as game features which obstruct your path until you have enough experience to pass them.
However, the whirlpools surrounding Whirl Island are most likely to be caused by Lugia, who resides deep within the Island. Lugia lives in the ocean and is rumoured to have the ability to create whirlpools even when it moves.
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In mahogany town in the team rocket hideout lance gives it to u
Whirl Islands only exist in Gold, Silver, Crystal, HeartGold and SoulSilver.
Pokemon Crystal only contained seven HMs. The 8th HM Rock smash isn't available until later generation games. The HM one can get in Pokemon Crystal are cut, fly, whirlpool, waterfall, strength, flash, and surf.
In Mahogany Town you have to go to the house north of the Gym and Pokemon Center (the one directly between the two). Lance will be there and so will Team Rocket. You've got to beat Team Rocket before Lance will give you HM06 Whirlpool.