fly is an HM and no Pokemon can forget an HM.
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The reasons why your Rayquaza isn't migrating to Diamond could be the following reasons: 1. Your Diamond game card or your Ruby game pak could be fakes. 2. You haven't unlocked the migration feature in "Diamond" yet. or 3. Your Rayquaza knows a HM such as Fly or is holding mail.
first you have to defeat Aqua\Magma and Then go to sootpolis city you wiil see Kyogre\Groundon Go to sky piler and go to the top dont worry they will be no cracks go up the stairs and go near Rayquaza It will fly . fly from the Rooftop use fly and go to sootopolis there there you will see amazing screenshots of Rayquaza Both Kyogre and Groundon Will go away and Rayquaza Fly away first you have to defeat Aqua\Magma and Then go to sootpolis city you wiil see Kyogre\Groundon Go to sky piler and go to the top dont worry they will be no cracks go up the stairs and go near Rayquaza It will fly . fly from the Rooftop use fly and go to sootopolis there there you will see amazing screenshots of Rayquaza Both Kyogre and Groundon Will go away and Rayquaza Fly away
The only pokemon to get fly by leveling up are Salamance and Rayquaza.
You will need to use TM02- Fly to teach it. The only Pokemon that can learn Fly naturally are Salamence and Rayquaza.
fly is an hm. no Pokemon learns it by lvling up. except rayquaza