You can find Lugia (if you're playing Alpha Sapphire) by interacting with the portal if you have the Tidal Bell. In Omega Ruby this portal will not appear.
You also find the Scanner here (if you have talked to the scientist outside) regardless of which version you are playing, which is required to get Lugia (AS)/Ho-Oh (OR). You need to give the Scanner to Captain Stern in the Slateport Harbor (in Slateport City), who will give you the Tidal Bell (AS)/Clear Bell (OR), the item that causes portals containing the Generation 2 cover legendaries.
Note that the item is invisible and might be on a slightly different tile than someone else's, but this shows where the general location should be near.