Collect piece of time which spawn rarely underground near diamond level.
Collect all 9 to make the adamant orb and right click it in extreme hills to spawn Dialga.
Palkia
Collect piece of space which spawn rarely underground near diamond level.
Collect all 9 to make the lustrous orb and right click it in the ocean to spawn Palkida
Giratina
Collect piece of shadows which can be dropped rarely by any ghost pokemon
Collect all 9 to make the griseous orb and right click it in the night to spawn Giratina
Zekrom
Collect the dark stone
Dark stone can be found underground very rare since it is only 1 item
Right click it during a thunderstorm
Reshiram
Collect the light stone
Light stone can be found underground very rare since it is only 1 item
Light stone can be found underground
Right click it in the morning near a fire source within 5 blocks
Kyurem
Spawns in ice mountains with a very rare chance during a snow storm
Deoxys
Spawns in the end at a rare chance
Heatran
Spawns in the nether near lava with a rare chance
Groudon
Spawns in the nether with a rare chance
Kyogre
Spawns in the ocean with a rare chance while raining
Lugia
unknown
Ho-Oh
unknown
Shaymin
spawns in forest with a rare chance
Celebi
Spawns in forest with a rare chance
Darkrai
Spawns in the night in plains with a rare chance
Cresselia
Spawns in the morning in the plains with a rare chance
Jirachi
Spawns in the night in the forest hills with a rare chance
Rayquaza
Spawns in extreme hills with a rare chance
Latios
unknown
Latias
unknown
Regice
unknown
Regirock
unknown
Registeel
unknown
Regigigas
unknown
Suicune
unknown
Raikou
unknown
Entei
unknown