How to make the team aqua leave lilycove
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That pretty vague so I'll try to start from when you first reach Lilycove.
When you get there, go to the Pokemon center and get a surfing Pokemon, and head back into the route you came in on and there should be a dock under the Safari Zone, surf off of there and go into that big mountain (Mt. Pyre) and head towards the top. After thats all said and done, you gotta head towards the bases. I think they're open at the same time, but if you still can't get into Lilycove caves base for Team Aqua, head to the Jagged Pass (ride the little rail car up the mountain to Lavaridge) and there was a Magma member standing there before, well, he's gone now and the Magma Emblem you obtained should open up their base.
After you beat that, head back to Lilycove and beat the Aqua base and the route to Mossdeep should be open.
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