With Secret Slab/Mystery Part Zapdos: Amp Plain 7F
Mewtwo[Darkness]: Dark Crater 6F, (and another location)
Raikou: Concealed Ruin 20F
Entei: Deep Dark Crater 10F
Lugia: Surrounded Sea 18F
Ho-oh: Mt.Mistral 19F
Celebi: Mystifying Forest 10F
Latias: Spacial Rift 10F, Happy Outlook 10F
Latios: Deep Spacial Rift 5F, Midnight Forest 24F
Deoxys: Shimmer Hill 17F (appear in Temporal Tower as non-recruitable mirage if has SS/MP)
Darkrai: Mystifying Forest 13F, Deep Crevice Cave B2F, Miracle Sea B3F, Mt. Travail B17F, Spacial Rift B14F
Without SS/MP Giratina: World Abyss 30F
Kyogre: Bottomless Sea 50F
Rayquaza: Sky Staircase 50F
Groudon: Shimmer Desert 10F
Aritcuno: Mt. Avalanche 20F
Mew: Mystery Jungle 30F
Heatran: Giant Volcano 20F
Jirachi: Final Maze (Makuhita dojo) 23F
Suicune: -(ditto)- 29F
Moltres: -(ditto)- 40F