Instructions
Play and finish "Destiny Odyssey," the first accessible story mode. You can use any of the available characters. Upon completion "Shade Impulse" story mode will be unlocked.
Play and finish the "Shade Impulse" story mode with any of the available characters. In this mode you battle bosses from the main story mode again before a final battle against "Chaos." Complete this mode to unlock the "Duel Colosseum" mode, which is where "Spirit Stones" are found.
Select the "Airship Course," the first course in "Duel Colosseum." Keep fighting random enemies until you receive a "Spirit Stone" or three "Dusty Elixir."
Press the "Triangle" button to access your character customization menu. Scroll down using the "D-pad" then highlight "Shop" and press "X."
Press the "R" (right trigger) button until you reach the "Accessories" menu. Scroll down to "Spirit Stone" using the D-pad then press "X." If you have three dusty elixirs you will see the words "TRADE" next to the item and the elixers will be traded for the "Spirit Stone."
Keep fighting on the Airship Course to build up your collection of spirit stones. which you can then use from the customization menu to upgrade your characters weapons.