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Ho-oh, Lugia, Moltres (Mt. Silver), Articuno, Zapdos, Mewtwo, Entei, Raikou, Suicune, Kyogre, Groudon, Rayquaza (Found in the Embedded Tower; Latias and Latios required for two of the three [Latias for Kyogre, Latios for Groudon, both for Rayquaza; Must beat Red first], trading is required for the Eon not in your game [Latios in HeartGold, Latias in SoulSilver], also requires Red Orb for Kyogre, Blue Orb for Groudon and Jade Orb for Rayquaza)
Through Special Events