Pokemon news from Down Under.
When you finally find the sapphire on Seven Island it is immediately stolen from you by a scientist who intends to sell it to Team Rocket. To get it back from the scientist head to the warehouse on Five Island and enter the two passwords. After defeating the Team Rocket members inside you will be able to battle the scientist and reclaim your sapphire!
By giving the ruby and the sapphire to Celio in the Pokemon Center on One Island you will be able to trade pokemon with the Ruby and Sapphire games!
The unknown dungeon is north of Cerulean City and is the location of the ultimate psychic Pokemon Mewtwo. To be able to enter the unknown dungeon you first have to defeat the Pokemon League.
There may be more quests that need to be fulfilled before the way into the unknown dungeon opens, such as getting the National Dex, but I am not sure.
Try beating the Pokemon League and if that doesn't work then more research is needed!