From Bulbapedia, the community-driven Pokémon encyclopedia.
The following information details the HeartGold and SoulSilver Legendary Pokémon.
If you happen to accidentally knock out a legendary, beating the Elite Four again will regenerate them. Entei, Raikou, Latias and Latios will appear in a random route and continue roaming.
Main article: Part 13.
Item Requirements: Rainbow Wing from the old man in Pewter City.
Go to the north of the town and enter the building to the north beside the Burned Tower. Inside, talk to the monk on the right and he will let you through if you have the Fog Badge (which you must have to reach Pewter City anyway). Go down the stairs into the passageway and up the stairs at the other end.
If you use the Dowsing MCHN here, you can find several TinyMushrooms and Big Mushrooms. Follow the trail to Bell Tower.
The only Wild Pokémon that you can get in Bell Tower are Rattata and Gastly.
Bell Tower 1F
Go up to the top left corner of the tower and talk to the monk. He will stop you from going up unless you have the Rainbow Wing with you.
Bell Tower 2F
Go to the bottom of the room and up the ladder.
Bell Tower 3F
Take the bottom left path and collect a Full Heal, then take the top right path back to the ladder and the top right path from there. Use the top left path to reach the center platform with the beam. If you use the Dowsing MCHN, there is a Max Potion near here. Go up five or six steps and cross the path to the right. Take the bottom right path and go up the ladder.
Bell Tower 4F
Take the path to the bottom of the ladder, but go left rather than down. Follow this path to collect an Ultra Ball. Follow the path that it was blocking, until you reach a PP Up. Follow the path to the left, completely ignoring the ladder, and use the top left path to reach another ladder platform. Again, ignore the ladder and collect the Escape Rope. You'll need it after catching Ho-Oh to get out, unless you took a Pokémon with Fly or Dig. Use the top right path to get to the center platform, and then the top left one to get to a ladder. This time, go up it.
Bell Tower 5F
Take the top right path and go straight right, then down to the center platform where you can find a Rare Candy. Use the right path and go down the ladder.
Bell Tower 4F
Go back up to the top-left corner of the room and take the same ladder up.
Bell Tower 5F
Take the top right path again but this time go down when the chance comes. Go slightly left and then straight down. Take the right path at the fork. When you reach a platform with a ladder, go up it.
Bell Tower 6F
Go straight up and collect the Max Potion, then across the log bridge to the right. Go right up to the top, take the upper path across and collect the Full Heal. Take the bottom left path and continue down until you get to a ladder. Go up it.
Bell Tower 7F
Take the path past the teleporter, collect the Max Revive and return to the ladder platform where you came up. Go to the teleporter at the top, which will take you to the center beam. Go into the other teleporter, which will take you to a higher floor.
Bell Tower Teleportation
Go down and take the first path across three hops, down one hop, and left three hops. Take the teleporter, then take the upper path left and collect a Nugget. Take the right path left and go back into the teleporter. Take the upper left path across, and follow it round to another teleporter. Enter it and it will take you to the center beam of one of the floors. Collect the Max Elixir and teleport back.
Take the path right onto the starting platform again, then go up to the top and teleport back to 7F. Take the other teleporter on the other side of the beam again. Take the path to the right, then down, then left, and take the teleporter. Go down a bit more and take the other teleporter.
Get the HP Up to the left and then take the teleporter on the far end of the platform. Go up across the log bridge. Ignore the teleporter but continue left. Collect the Full Restore and go back into the teleporter you just missed. You will be on the center platform. Take the ladder up.
Bell Tower 10F
Take the old plank bridge across, then go up the ladder.
Bell Tower Top
Go forward, and Ho-Oh will be there waiting for you. Talk to it to begin the fight. It has its own theme tune, too. Although it has been stated it above, if you accidentally knock out Ho-Oh, go back and beat the Elite Four to make it reappear.
No particular Poké Ball works best on Ho-Oh, but a Heavy Ball has a better result than most others obtainable.
Main article: Part 13.
Item Requirements: Silver Wing from the old man in Pewter City.
Make sure you have something with Surf and Whirlpool, then go left onto Route 40.
Keeping just next to the right wall, Surf down onto Route 41
Continue down, still just next to the right wall. When you get to a whirlpool, go just south of it and use Whirlpool to get across, then Surf up to the beach. Go round, Surf to the other side and go into the cave.
Most items in the Whirl Islands are only findable with the Dowsing MCHN, so I will not go into them here.
Whirl Islands 1F
Jump off the ledge a bit above, then follow the top path and jump off the ledge. Go down the ladder.
Whirl Islands B1F
Follow the path around and go down the ladder at the end.
Whirl Islands B2F
Go down to the sage and talk to him. He will let you through if you have the Silver Wing with you.
Go down the slope and enter the cave. Collect the Rare Candy below you, then come out again.
Continue down the slopes to reach another gap in the wall. Go through it.
Whirl Islands B3F
Go across to the other side of the room to Lugia. Surf over to it and talk to it to start the fight. Like Ho-Oh, it has some nice theme music.
Your best way to catch Lugia is to throw lots of Dusk Balls and hope for the best.
Raikou and Entei
You can track Raikou and Entei on your Pokégear after completing the Burned Tower. If you can't see one of them, it is most likely that their icon is underneath yours, meaning that they are on your Route. The best Poké Balls to use on them are probably Fast Balls or Quick Balls. Since they are roaming Pokémon the damage you do to them will stay done to them until it faints.
They will only roam in Johto and will not go past Route 40, so don't expect to fight them on anywhere west of Olivine City (Route 40, 41, 47 and 48) or east of New Bark Town (Route 1-28).
After seeing Suicune in Route 14, you can battle it in Route 25. Eusine will appear, and then allow you to battle it. Talk to it to begin the battle. It would be advisable that you use a Net Ball to capture it. If you have to regenerate it with the Elite Four, it will not re-appear in Route 25; it will re-appear in the Burned Tower and you can battle it there.
Articuno, Zapdos and Moltres
You will probably visit the Seafoam Islands, Kanto Power Plant, and Mt. Silver at some point in the game after getting the Earth Badge. When you do, you can find Articuno, Zapdos and Moltres respectively.
Mewtwo is at the end of Cerulean Cave. A description of how to get there is unnecessary since there is a map of Cerulean Cave on its page. But you still need to beat all Gyms in Kanto to get to it.
Groudon and Kyogre
After receiving the Kanto starter from Professor Oak (after beating Red at the top of Mt. Silver) go to Mr. Pokémon's house on Route 30. Mr. Pokémon will give you a gift: the Blue Orb in HeartGold, and the Red Orb in SoulSilver. Now Fly to Cianwood City.
Talk to Chuck, then go through to Route 47.
Follow the path into the Cliff Cave. Go down to the bottom floor, then exit onto the watery area. Surf as far left as you can; there is a gap in the rocks under the second bridge, in about the center.
Go up the Rock Climb slopes (there is a hidden Stardust between them). Go to the far left, Rock Climb down, pick up the Wave Incense, then Rock Climb back up and enter the cave.
Here you can find Kyogre in HeartGold and Groudon in SoulSilver.
Requirements: Kyogre/Groudon from your version and the other from another HG/SS cartridge.
Go and see Professor Oak. He will give you the Jade Orb.
Go back to the Embedded Tower. Rayquaza can now be caught.
Latios and Latias
At any point after returning the Machine Part to the Kanto Power Plant, Fly to Saffron City. Go up from the Pokémon Center about two streets on the left side. Enter the purple house. Go to the second floor of the house and talk to the girl. This is Copycat, who was lost her Clefairy Doll. Exit the house and fly to Vermilion City.
Enter the fan club just north of the gym. Talk to the fat person to get the Clefairy Doll. Don't return it to Copycat just yet, or you will miss out on the chance to get Latios or Latias.
Exit the building and talk to Steven Stone. You now have a chance to get Latias in HeartGold or Latios in SoulSilver. They are marked on your map similarly to Entei and Raikou.
Latias and Latios will only roam in Kanto, so don't expect to fight them outside Mt. Silver or anywhere west of Route 27.
Now return to Saffron City and return the Clefairy Doll to Copycat. She will exchange it for a Pass to use the Magnet Train from Goldenrod City to Saffron City and vice versa.