It just disappears until you beat the Pokemon League. Then it will reappear where you first saw it.
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When you catch dialga/palkia or defeat them, you can catch azelf and uxie in the lakes.Mespirit will flee so you gotta get a poketech radar to track it down.
After you catch the main legendary (dialga, palkia, giratina) go to lake verity and mesprit will be in the cave in the middle of the lake. Talk to it and then it will flee and appear on your map app.
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No, Dialga is not evil; Dialga is more of a hero. I'm sure Dialga are nice. Palkia is, however, sort of evil, and Giratina is evil, but Dialga is more of a protagonist.
Dialga is not in that Pokemon Emerald. Back when that game was made, Dialga didn't exist.