Moltres- Receive all 16 badges. Moltres is now in Mt. Silver at level 50. Requires Rock
Climb, Surf, and Waterfall.
Zapdos- Receive all 16 badges.  Zapdos is now by the Power Plant at level 50. Requires
Surf.
Articuno- Receive all 16 badges. Articuno is now deep in the Seafoam Islands at level 50.
Requires Surf.
Raikou- Roams Johto after encounter at Burned Tower. Check Pokegear map for location. At
level 40.
Entei- Roams Johto after encounter at Burned Tower. Check Pokegear map for location. At
level 40.
Suicune-Find in the following places after encounter at Burned Tower: North of Cianwood,
middle entrance of Mt. Mortar by Apricorns, after getting off the S.S. Aqua, Route 14 on
the way to Fuchsia City, and it will be on the cape on Route 25 after beating Misty. If
you defeat it, beat the Elite Four again and it will be in the burned tower. At level 40.
Lugia-If you have Soulsilver, receive Silver Wing from the Radio Tower Director in
Goldenrod after defeating Team Rocket. Beat Kimono Girls in Ecruteak City Dance Theater to
receive the Tidal Bell. Lugia is in the Whirl Islands. Show the Silver Wing to the monk
guy to find Lugias domain. It is at level 45. If you have Heartgold, an old man on a hill
in Pewter City gives you the Silver Wing. You dont need the Tidal Bell. Lugia is in the
Whirl Islands. Show the Silver Wing to the monk guy to find Lugias domain. It is at level
70. Requires Surf and Whirlpool.
Ho-oh- If you have Heartgold, receive Rainbow Wing from the Radio Tower Director in
Goldenrod after defeating Team Rocket. Beat Kimono Girls in Ecruteak City Dance Theater to
receive the Clear Bell. Ho-oh is at the top of the Bell Tower. Show the Rainbow Wing to
the monk guy to find Ho-ohs domain. It is at level 45. If you have Soulsilver, an old man
on a hill in Pewter City gives you the Silver Wing. You dont need the Clear Bell. Ho-oh is
at the top of the Bell Tower.. Show the Rainbow Wing to the monk guy to find Ho-ohs
domain. It is at level 70.
Mewtwo- Receive all 16 badges. Go to Cerulean City and go north up the bridge. Then turn
left and go down through the grass. Surf down and then left to find the cave. Mewtwo is at
the bottom at level 70. Requires Surf and Rock Smash.
Kyogre- Receive all 16 badges. Need to have beaten Red. In Embedded Tower. Heartgold only.
Receive Blue Orb from Mr. Pokemon. At level 50. Requires Surf.
Groudon- Receive all 16 badges. Need to have beaten Red. In Embedded Tower. Soulsilver
only. Receive Red Orb from Mr. Pokemon. At level 50. Requires Surf.
Rayquaza- Receive all 16 badges. Need to have beaten Red. In Embedded Tower. Need opposite
legendary form other game (has to be from Heartgold or Soulsilver). Receive Jade Orb from
Mr. Pokemon. At level 50. Requires Surf.
Latias- Roams Kanto after receiving the Lost Toy at the Fan Club in Vermillion. Steven
(Hoenn Champion) will tell you. Only in Heartgold. Check Pokegear map for location. At
level 35.
Latios- Roams Kanto after receiving the Lost Toy at the Fan Club in Vermillion. Steven
(Hoenn Champion) will tell you. Only in Soulsilver. Check Pokegear map for location. At
level 35.
Giratina, Palkia, Dialga- Bring an event Arceus to Ruins of Alph. Cynthia will tell Arceus
to create one of those 3 legendaries. At level 1.
Wow that was long! I hope I helped!