Give the Scanner to Captain Stern
He will give you a Clear Bell in OR and a Tidal Bell in AS.
Take the Bell (depending on your version) to Sea Mauville
What to do with the Bells
After you arrive at Sea Mauville go to the Deck in OR and in AS go to the Underwater Basement . The bell will start to resonate and cause a portal to appear.
Go up to the Portal and press "A". In OR Ho-Oh should appear and battle you and in AS lugia will.
Before you interact with the Portal remember to Save :D