>>38521002During the cutscene if you press Up on the circle pad at the exact frame you collide with the boulder Mega Rayquaza will steer off course and land on the moon while Deoxys' tentacles are shown coming out of the triangle from the smashed boulder. It's why you can defeat Deoxys and go back for it later since that's what was intended until Ishihara realized companies wanted to pay for Jirachi distributions instead. You only get one chance at this though so if you miss the frame you need to hit you'll have to buy a new cartridge because the cutscene burns the cartridge's fuses enabling this chance.
