Legendary Pokémon Appearances

When you have cleared the game and return to areas, there is a small chance that you will encounter various Legendary Pokémon. When you encounter these Pokémon, you will get into a boss fight and will have to defeat them in order to both proceed and attempt to obtain the Pokémon. You will note the encounters by the fact that the springboard that sends you to the boss room will be shiny. These Pokémon take the place of the boss for that level that time
Most of these appearances are not restricted to certain levels but in fact certain types ofs across all levels. These appearances are very rare, appearing for 5% of the boss battles, and may require numerous visits before it occurs. Some Pokémon have pre-requisites to appear, however all require you to defeat the Dark Rust and finish the story. The Pokémon are as follows

No. Pic Name Type Area Found
Mewtwo All Factorys
After Completion of Battle Royale EX-6
Lugia All Beachs
Ho-Oh 3-2 Volcanic Slope - Autumnwood
3-3 Firebreathing Mountain - Autumnwood
Latias All Meadows
Latios All Meadows
Kyogre All Beachs
Groudon All Magmas
Rayquaza All Towers
Deoxys All Factorys
Dialga All Caves
Palkia All Lakes
Heatran All Magmas
Regigigas All Deserts
Giratina All Horrors
Giratina All Horrors
Cresselia All Treetops
Darkrai All Horrors
Arceus All Towers
After completion of Team Battle EX-6
Cobalion All Caves After defeating Terrakion & Virizion
Terrakion All Canyons
Virizion All Forests
Tornadus 3-2 Volcanic Slope - Autumnwood
Requires 3 Encounters Before Battle
Thundurus 3-3 Firebreathing Mountain - Autumnwood
Requires 3 Encounters Before Battle
Reshiram All Caves
Zekrom All Caves
Landorus 3-2 Volcanic Slope - Autumnwood
Requires defeating both Tornadus and Thundurus
Kyurem All Glaciers