When you return to Pallet Town, Professor Oak is so impressed with your accomplishments that he offers you a choice of one of the three Kanto starter Pokémon as your own. Choose whichever you like, but you will need an empty party slot to accept it.
Make a return trip to Saffron City and visit the Silph Co. building. Talk to Steven near the front desk, and he asks you a question: Of a group of stones in front of you, would you choose the green stone, the red stone, or the blue stone? The answer you give determines which Pokémon he offers you. Treecko, Torchic, and Mudkip are the starter Pokémon of his native Hoenn region.
Once Steven leaves, follow him to the Pewter Museum. Enter the building to find him viewing one of the exhibits while muttering about the stars in the night sky. When he leaves, follow him back to the Silph Co. building.
Time for a Trade
Speak to him and he asks to trade Pokémon. He is looking for a Forretress, and is willing to part with his Beldum. Beldum can only be found in the Safari Zone, while Forretress are unavailable in the wild and must be evolved from a Pineco. Beldum will eventually evolve into the powerful Metagross, and Steven has given this one a Dawn Stone to hold.
As the player should have received the Silver Wing in Pewter City, proceed to the Whirl Islands to capture Lugia. Lugia will not let itself be caught easily, so be sure to stock up on your favorite type of Poké Ball. 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.
There are many items to be found throughout the caves, but if you are only looking for Lugia, start with the northeast 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.
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 find Lugia waiting in front of the waterfall. Make sure you save before battling if you are trying to capture, in case Lugia faints.
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. If you happen to knock it out, it will reappear if you again beat the Elite Four.
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.
The only items accessible from the southwest island are the Escape Rope and the Calcium, both of which would have been collected already.
As the player should have received the Rainbow Wing in Pewter City, proceed to the Bell Tower in Ecruteak City to capture Ho-oh. Ho-Oh will not let itself be caught easily, so be sure to stock up on your favorite type of Poké Ball. Repels, Escape Ropes, and Pokémon with status-inflicting moves, like Spore or Thunder Wave, are also recommended. Head north from the Dance Theater to reach the Barrier Station. Flash the Fog Badge to reach Bellchime Trail. On the trail, speak to Morty. He will tell you that Ho-oh did not choose him and asks if you would help him in his training. Add his phone number if you wish to battle him again. Then proceed to the Bell Tower.
As you approach the back of the first floor, the Rainbow Wing suddenly floats up into the air. Seeing the shimmering rainbow feather, the monk finally moves from the ladder.
Go west to reach a Full Heal. Move around in an S-shape to reach the northeast stairs.
Go south to find an Ultra Ball, and south again to get a PP Up. Grab the Escape Rope in the southwest, then climb the northwest stairs.
Bell Tower, 5F
Bell Tower, 6F
Work your way to the pillar for a Rare Candy. The ramps here keep you from advancing, so take the southeast stairs and backtrack through 4F. Stay to the west of the pillar to reach the stairs in the south.
6F has a simple layout that serves as a transition between the ramps on the lower floors and what lies above. The next three floors use a series of warp tiles for quick navigation. First grab the Max Potion, then circle around to the northwest corner to get the Full Heal. Take the stairs up to 7F.
Bell Tower, 7F
Bell Tower, 8F
Step on the nearest warp tile to reach the pillar, and take the next to reach the east wall of 9F. There are two warp tiles to the south; the right one leads to the center of 8F and a Max Elixir, while the left one leads to the south side of 8F and a Nugget. Backtrack to the first warp on 7F, grab the Max Revive to the northeast, and go south to take the next warp to the west side of 8F.
The next warp takes you to the north side of 9F where you can find an HP Up, and the next warp tile on 9F brings you back to the east side of 8F. Pick up the Full Restore to the northwest and take one last warp to the center of 9F.
Bell Tower, 9F
Bell Tower, Rooftop
Climb the stairs to reach the rooftop.
Climb the golden stairway to reach the tower's rooftop, where Ho-Oh will be waiting for you. Make sure you save before battling if you are trying to capture, in case Ho-oh faints.
Start off by using status-inflicting moves, like Spore or Thunder Wave, to wear it down. Follow up with Water- or Electric-type attacks to inflict double the damage. Use caution with Rock-type attacks, as Ho-Oh takes four times the normal damage from such moves. Then slowly chip away at its remaining health with Fire-, Grass-, Fighting-, Bug-, or Steel-type attacks, as moves of these types only inflict half- or quarter-damage. If you happen to knock it out, it will reappear if you again beat the Elite Four.
Near the entrance to the ruins, a Hiker informs you of their history. Ages ago, the Embedded Tower was constructed deep into the cliffside, and its peak was said to touch the sky. It is believed that it also ran far below to the ocean floor, as well. In short, the ruins formed a link between the land, the sea, and the sky. Enter the chamber to find the legendary Pokémon KyogreHG / GroudonSS silently watching as you approach.
Add the ancient Pokémon to your party and pay a visit to Professor Oak. He is amazed that you have caught one of these powerful Pokémon, but he always thinks of Kyogre and Groudon as a pair; wherever one appears, the other must not be far away. Since you have one already, he wonders if you could bring both to him. However, Groudon only shows itself to those with shining-silver spirits, while Kyogre only appears to those with golden hearts. Find a Trainer that matches this description and trade for the second Pokémon. When you show the pair to the professor, he rewards you with the Jade Orb, which calls the third member of the Hoenn myth to the Embedded Tower.
Embedded Tower, as seen when occupied by Rayquaza
As Rayquaza is related to the other two super-ancient Pokémon, its Ability is also involves the weather; however, Air Lock eliminates the effects of all weather conditions. Its Outrage attack is powerful enough already, but can become even more destructive if AncientPower is able to raise its stats. Begin with Rock- and Dragon-type attacks to wear it down quickly. Ice-type attacks are extremely effective, as well. After that, switch to Grass, Fire, Water, Bug, and Fighting moves to weaken it further. Ultra Balls, Dusk Balls, and Heavy Balls are especially useful. If you fail to catch it, defeat the Pokémon League once more to cause it to reappear.