Instructions
Complete the game and after the credits are finished check your mailbox for random missions. Look for missions that list the reward as "Friend Area" and do these until you get the "Dragon Cave" friend area. This also automatically unlocks the "Wyvern Hill" dungeon.
Travel to the "Wyvern Hill" dungeon making sure to take a key with you. If you don't have a key you can find one in the "Solar" or "Western" dungeons. Keys are randomly found on the dungeon floors so you have to explore until you get one. Keys are generic and can be used on any locked door. However, they are lost after it is used. The Western Cave dungeon has ninety nine floors, so bring along an escape rope so you can make a easy exit as soon as you find a key on one of the floors.
Make your way through the dungeon until you reach the 30th and final floor. Use the key to open the door and inside you will find HM Fly. Press the "B" button then highlight "Items" and press "A." Scroll down to "Fly" and press "A" again. Highlight "Use" then press "A" and choose the Pokêmon that you want to use the move. As soon as you use "Fly" you will be shown a map and can choose your destination (in this case Sky Tower) to instantly go there.