Give the legendary pokemon an effective status problem besides confusion then get their life down to the last bit of life. Now use you're Ultra Balls or Master Ball. If you're fighting Mewtwo use you Master Ball, but you have to get them in red on the life bar and you have to give them a status problem no matter what if you don't and you didn't copy the Master Ball. Then you can can use Ultra Balls, they work too. Also make sure you have room in your box.