First, after defeating team aqua at Weather Station and getting the wind Badge from Winona, go down. It will be a long way down. Then, after passing the safari, go all the way down. Use surf. It should take you to an island, the Mt. Pyre. team Aqua was scattered everywhere the Mt. Pyre. Then wanted to get the Red Orb and control Kyogre. Climb all the way up the mountain. Remember to keep away from team Aqua. Then on the top, after a short battle, they will still steal the Red Orb. Then, the Man who protect the orb will give you the blue orb to balance the peace. Then go all the way to the Lilycove. Then get inside the hideout.
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The Team Aqua boss is in the Team Aqua Hideout northeast of Lilycove City. You will need the HM move Surf to reach the hideout.
You get it in The Team Aqua Hideout by Lilycove City.
you get it in team aqua/magma's hideout in lilycove
team aqua hideout at lilycove city
team magmas hideout is where you go down from the cable car, east of lavaridge. aqua is a surf north away from lilycove or mossdeep, i forgot sorry.