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If so, does it randomize the nature so I can soft reset for it easily? I really don't want to go through catching Rayquaza and Deoxys just to roll for 2 good natures on each of them.


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Best answer

Yes :D

Almost every single legendary can respawn after you defeat the E4.
You can also Soft-Reset for Deoxy's nature as well

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Wait, what legendaries DON'T repawn then?
I think Rayquaza because you must catch it to go forward in the story, so technically it doesn't because it's a one time catch thing.
That makes sense.
Also pokemon MD ones.