The Legendary Tower Duo, Ho-oh and Lugia come from the Johto region in Pokémon Silver and Gold have been with us on our Pokémon journey for quite a while and neither of them are looking to jump ship any time soon.
Ho-oh and Lugia are not Legendary Pokémon that appear at random in Mirage Spots (those shiny spots you see while soaring), they are unlocked through various (and somewhat specific) actions. Seeing as they are unlockable Legendaries, you can have them before your encounter with the eighth gym leader in Pokémon Omega Ruby and Alpha Sapphire.
In order for you to catch Ho-oh and/or Lugia you will need a Pokémon with Surf, for the Primal Kyogre and Groudon event to have occurred, and you will need to make use of the trade feature if you want them both in one game because they are specific to each version.
The first step in unlocking these the Tower Duo is to Surf East of Dewforth City to Sea Mauville on Route 108. Follow Route 108 to the abandoned ship, once there explore down to the control room (you will have to move through water to get there). In the control toom you will find a Key Item called the 'Scanner.' Take the item to Slateport City's docks and talk to Captain Stern (he's wearing green and stand near a ship). Stern will take the item and give you either the Tidal Bell or Clear Bell — which item you get depends on with version of the game you are playing.
Omega Ruby:
- Clear Bell
- Ho-oh (level 50)
Alpha Sapphire:
- Tidal Bell
- Lugia (level 50)
Take your newly obtained item back to the abandoned ship on Route 108. Arriving at the ship will trigger an event where the item you obtained from Stern will begin to glow. If you have the Clear Bell you will see a portal on the deck of the ship, interacting with the portal will lead you to and encounter with a level 50 Ho-oh. If Stern gave you a Tidal Bell, head down to the control room – you will find a portal there that will take you to an encounter with a level 50 Lugia.
Good luck and remember to bring HP restoring items!
Here's where you can find more guides for catching legendary Pokémon and finding Mega Stones.
