This is the Bulbapedia walkthrough for Pokémon HeartGold and SoulSilver.
These pages follow the remade Nintendo DS iteration, not Pokémon Gold and Silver. The guide for those games can be found here.

Lugia Emerges from the Waterfall BasinSS

Suddenly, their younger sister enters the building and claims that she just saw the shadow of a big Pokémon in the Whirl Islands' waters. The sisters run off, leaving you to follow. Lugia will not let itself be caught easily, so be sure to stock up on useful Poké Balls, such as Heavy Balls. Repels, Escape Ropes, and Pokémon with status-inflicting moves, like Spore or Thunder Wave, are also recommended. Fly back to Olivine or Cianwood and sail out into the ocean. Surf and Whirlpool are required to fully explore the islands' underwater cave network; Strength and Flash are helpful, but not necessary.

Route 41

Surf east from Cianwood City to get to Route 41. There are some more swirls of water that need to be traversed in order to get to the Whirl Islands. Before we do that, don't forget some items on the sand.

Whirl Islands

There are many items to be found throughout the caves, but if you are only looking for Lugia, start with the northeast island.

Available Pokémon

1F, B1F, B2F Pokémon Games Location Levels Rate HG SS 22-24 50% HG SS 23 30% HG SS 22-24 15% HG SS 23 5% Surfing HG SS 15-25 60% HG SS 10-20 30% HG SS 15-25 10% Fishing HG SS 10 95% HG SS 10 5% HG SS 20 60% HG SS 20 37% HG SS 20 3% A colored background means that the Pokémon can be found in this location in the specified game. A white background with a colored letter means that the Pokémon cannot be found here. B3F Pokémon Games Location Levels Rate HG SS 23-25 50% HG SS 24 30% HG SS 23-25 15% HG SS 24 5% Stationary Pokémon HG SS Only one 45, 70 One A colored background means that the Pokémon can be found in this location in the specified game. A white background with a colored letter means that the Pokémon cannot be found here.

Whirl Islands, northwest interior Whirl Islands, northeast interior Whirl Islands, southeast interior Whirl Islands, southwest interior Whirl Islands, B1F Whirl Islands, B2F Whirl Islands, Waterfall Basin

Northwest Island

Step inside the cave, and take the ladder to the floor below.

Walk down the stairway to reach a hidden Pearl to the northeast, and a Full Restore to the south. Jump the ledge and climb the stairway to the east in order to reach a Nugget and a hidden Super Repel. Head east and jump the two ledges to reach a ladder; this leads to a dead-end with an Ultra Ball. Go south, jump another ledge, and backtrack to the first ladder in the northwest corner. Head south along the upper level to reach a Carbos, and climb down the ladder to the southeast.

Grab the Max Elixir and Full Restore from this dead-end area, then use an Escape Rope to exit the cave.

Northeast Island

Walk east, jump the ledge, and take the northern path to reach the next part of the main cavern.

Follow the rock platform southward, collect the hidden Revive, and climb down the ladder to B2F.

Inspect the north wall for a hidden Full Restore, then grab the Max Revive to the west. Speak with the monk, and the Silver Wing suddenly floats up into the air. When he sees the shimmering silver feather, the monk allows you to pass. Step through the archway just south of him to reach a Rare Candy. Continue the climb down the cliffside to reach another archway, where your lead Pokémon retreats into its Poké Ball.

Step inside the waterfall chamber and climb onto the platform, where you find the Kimono Girls waiting for you. Zuki tells you that once their mystical dance combines with the sound of the Tidal Bell, Lugia will emerge from the waterfall basin once more. The Tidal Bell floats up above you, and the sisters begin their dance. The two other bells, fastened on either side of the waterfall, also activate. As if drawn by the peal of the bells, Lugia emerges from behind the waterfall.

HeartGold players are unable to challenge Lugia until after obtaining the Silver Wing in Pewter City. The Tidal Bell is not required.

Lugia

SAVE your game before challenging Lugia.

Start off by using status-inflicting moves, like Spore or Thunder Wave, to wear it down. Follow up with Rock-, Ghost-, Electric-, Ice-, or Dark-type attacks to inflict double the damage. Then slowly chip away at its remaining health with Fighting-, Grass-, or Psychic-type attacks, as moves of these types inflict only half- or quarter-damage. Because Lugia is over 205 kg, Heavy Balls are the second-most effective Poké Ball (other than the Master Ball). If you happen to knock it out and don't want to soft reset, it will reappear once you have entered the Hall of Fame.

SoulSilver Held item: None Lugia Lv.45

Southeast Island

Check the northwest corner for a hidden Rare Candy, then take the ladder down to the main cavern.

Head north along the rock ledge to find a Calcium. Go down the stairway and loop around to the west. Search near the south-central ladder for a hidden Ultra Ball, then move the nearby boulder northward. Head west to reach an Escape Rope, then climb the southwest ladder.

Detour across the pool of water to the east to collect another Ultra Ball, then take the exit to emerge on the southwest island.

Southwest Island

The only items accessible from the southwest island are the Escape Rope and the Calcium, both of which would have been collected already.

Ruins of Alph

Ruins of Alph (optional)

The ancient Ruins of Alph are believed to date back at least 1,500 years. Some chambers are accessible from Routes 32 or 36, and others are accessible from Union Cave. Most of the ruins can be explored using only Surf, but picking up all the items requires more moves, items, and a Pokémon. The script seen in these crumbling structures is the earliest known writing system in the world, but it is unclear which appeared first, these characters or the Pokémon that resemble them.

Available Pokémon
Outside Pokémon Games Location Levels Rate HG SS 18-24 90% HG SS 20-22 10% Surfing HG SS 10-20 60% HG SS 10-25 40% Fishing HG SS 10 15% HG SS 10 85% HG SS 20 40% HG SS 20 60% Rock Smash HG SS 3-14 100% A colored background means that the Pokémon can be found in this location in the specified game. A white background with a colored letter means that the Pokémon cannot be found here.

North chamber

Pass through the ancient structures to enter the northern chamber. Read the hint to identify the Pokémon, and move and rotate the pieces to reconstruct the puzzle, which glows briefly when completed. The floor gives way, dropping you into the main underground chamber where the first ten forms of Unown, A through J, have awakened. Shortly after, you are greeted by a young researcher. He is so impressed that you solved the first puzzle that he hands over the Unown Report, which automatically records any caught Unown.

Tuning into the Mysterious Transmission will improve the chances of meeting an Unown form that you have not yet encountered. This is also one of the few places where wild Natu and Smeargle can be found.

The Four Puzzles

Chamber Requires Hint Pokémon North N/A This Pokémon hides on the seafloor and watches the shore with eyes on its back. Kabuto Southeast HM03 A Pokémon that knew no fear and flew as it pleased through the skies long ago. Aerodactyl West HM03 This Pokémon, with feathers of seven colors, flies through the sky, according to legend. Ho-Oh Southwest HM03, HM04 A ten-legged Pokémon that swims on the bottom of the sea and eats plankton. Omanyte

The Four Panels

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