Yes you can. You just have to beat the elite four and then go back to his chamber. If you make him faint again do the same as last time. He will keep coming back if you make him faint until you catch him. :)
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moltres is in leaf green and fire red not emerald.
Moltres is in Mt. Mortar
Moltres is a legendary Fire and Flying type Pokemon. It does not appear in Pokemon Gold, but may be traded over from a first generation game. In the reboot of Pokemon Gold, Pokemon HeartGold, Moltres is encountered in Mt. Silver.
Moltres, the legendary Fire/Flying type of Kanto, has the Pokedex number 146.
Moltres is a legendary fire type of Pokémon in the Pokémon series. It is indeed possible to catch one with a great ball.