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You should use it on one of the 'roaming' pokemon, like Cresselia in Diamond/Pearl/Platinum.
No but i have heard that you can use it like a master ball on latias
Use a master ball. Unlike Mesprit, they'll run away from you before you can use Mean Look. They also know Roost which heals their HP making them even harder to catch. To catch all three with a master ball get Diamond/Pearl. You also need another DS. Once you get the master ball from Cyrus in Diamond/Pearl have one of your Pokemon hold it in that game then trade that Pokemon, take the ball from it then trade it back if you want. If you saved the master ball in Platinum BOOM you already have two! After that delete your Diamond/Pearl game then do the same thing again. If you don't have another DS then use the master ball on the one you want the most and try to use quick balls on the other two. actually mate if you use mean look it will work as long as the pokemons speeds high enough
no, you don't have to use your master ball on it. you could use it for any legendary Pokemon like mewtwo, or... you know what i mean!
When you have defeated the elite four go to the new island and work your way up to stark mountain heatran may not be there. The second time you go to stark mountain heatran will be there. I wouldn't use the master ball for heatran I used my master ball to get giratina.