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Capturing a boss seems random, like everything else. The catch rate seems somewhere between 1/50 and 1/100, although bosses might have a higher catch rate than regular pokes (from all the youtube videos I have seen).
The only "sure fire way" seems to be stunning a pokemon (in which stars shoot from their heads and a loud noise is made similar to when catching a pokemon) but this also seems to be random and rare. I have never seen this happen to a boss, though.
Also, I have read that you always catch a sparkling pokemon (maybe referring to the ones with abilities?) Maybe the ones you stun are the sparkly ones...I don't know. I don't have the game, I've just seen videos on youtube, and I've never seen one sparkle (but maybe its just the video quality).
Yup, capturing a Pokemon with sparkles (they don't always have abilities by the way) is guaranteed, but finding sparkling ones at all is a random as capturing a regular one from the final hit.
I've only ever managed to "stun" a boss a few different times, but when I managed to beat them before they got unstunned, they did get captured like regular Pokemon do. If you happen to have a Pokemon that's good at stunning (again, I don't know if it's even possible to be "good" at it or it's just another random thing), then try using it against bosses.
Hey man, LlamaGuy did encrypt the passwords. With what? ROT-13? -CJayC