You use whirlpool, a field move HM, to get past whirlpools. You have to defeat a certain gym leader and get a certain badge to use whirlpool in the field (outside of battle).
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You use whirlpool in two main areas. When you have to take the test with the elders in the Dragon's Den, you need Whirlpool. When you want to capture Lugia, you have to use Whirlpool to get into the islands.
you need the HM whirlpool (whitch you get it at mahogany town when you shut down the machines lance will give you it)
You need HM whirlpool to get that: You will have to investigate the gyarados rampage at the lake of rage while teaming up with lance and chase off the team rocket from the secret base in mahogany town. after the chase off mission is completed, lance will give you the whirlpool hm.
Well, if you have a Pokemon that knows whirlpool, you can go back to route 41 and go to the mysterious Whirlpool islands.
whirlpool is not classified as a HM in that Pokemon series, only in heartgold/soulsilver is it a HM, in diamond it is only a simple TM (1use)