Once you defeat Moltres in the game, it disappears and you can't catch it again. There are no ways to re-encounter it in the main story.
However, you can obtain Moltres via:
* Trading: You can trade with other players to get a Moltres.
* Events: Niantic has sometimes released Moltres in Pokemon GO events, though this is not related to SoulSilver.
* Breeding: After catching a Moltres, you can breed it with other compatible Pokemon to potentially get an egg that will hatch into a Moltres.
Let me know if you have any other questions!