Getting the Ruby
Defeat the Elite Four. In order to get the Ruby and Sapphire to connect to Hoenn, you'll need to beat the main story by defeating the Elite Four. This will require all of the Gym Badges and a strong team of Pokémon (at least level 60 or above). See this guide for tips on defeating the Elite Four.
Complete the National Pokedex. Another requirement you'll need to fulfill before getting the Ruby and Sapphire is obtaining the National Pokedex. This means you'll need to have logged 60 different Pokémon species in your Pokedex. Once you've seen at least 60 different types of Pokémon, talk to Professor Oak to receive the National Pokedex. This will make Pokémon from the Hoenn region start to appear in the game.
Take the ferry from Vermilion to One (Knot) Island. In order to get the Sapphire, you'll need to get the Ruby first. Talk to Bill at the Cinnabar Island Pokémon Center about visiting the Sevii Islands if you haven't already, then take the ferry from Vermillion to One Island.
Talk to Celio to learn about the Ruby. Find Celio in the Pokémon Center and speak to him about his machine. He'll inform you that he needs the Ruby, and will give you a pass to the first three islands (if you haven't gotten it from him already). If you haven't taken the Meteorite to Two Island yet, you'll need to finish that quest first.
Make your way to Mt. Ember. You'll be able to find the Ruby at Mt. Ember, located on the same island. Make sure that you have a Pokémon that knows Strength and a Pokémon that knows Rock Smash.
Learn the first Rocket Password. You'll overhear two Team Rocket members talking about taking treasure back to the Rocket Warehouse. You'll discover that it requires to password to enter, and the Rocket Members will accidentally spill the beans on the first: "Goldeen need log". Enter the cave after they take off.
Take the Ruby Path. Make your way to B5F at the bottom of the cave to find the Ruby. You can find the way down in the southwest corner of B3F. You'll find the Ruby in the middle of the room on B5F.
Collect the Ruby and return it to Celio. Take the exit on B3F for a quick route back to Celio. He will inform you that he needs another gemstone to make the machine work, and will give you a pass that let's you access all of the islands.
Finding the Sapphire
Head to Four (Floe) Island. On your quest to find the Sapphire, you'll need to stop at Four Island. Here you'll learn the location of the Rocket Warehouse. As you approach Four Island, you'll see your rival on the beach taunting you.
Make your way through Icefall Cave. The entrance to the cave can be found in the northeast corner of the island. You'll need to use Rock Smash to access the island first. When you enter the Icefall Cave, be wary of the icy patches on the floor. When you step on them twice, you'll fall to the floor below. Deliberately fall through the ice on the north side of the first floor of the cave. Climb back up the ladder, then purposefully fall through the eastern piece of ice in the new area. Slide down the ice then climb up the ladder. After climbing the ladder, fall through the southern piece of ice. Skate up, then right, then down and then fall through the ice again. Get the Waterfall skill and teach it to one of your Pokémon. Go up the waterfall in the previous cave using your new skill, and then go down the ladder to find Lorelai.
Help Lorelai beat the Rocket grunts. Battle the Rocket Grunts with Lorelai, and you will learn that the Rocket Warehouse is on Five Island. Unfortunately, you still only have the first password.
Visit Six (Fortune) Island and find the Dotted Hole. You can find the entrance to the Dotted Hole in Ruin Valley at the south end of the island. In order to enter the Dotted Hole, you'll need to use Cut on the door.
Solve the Dotted Hole maze. The Braille signs in Dotted Hole will tell you where to go, or you can just read the answer here. Drop through the hole when you first enter Dotted Hole. The signs will show the direction you need to go. To solve the maze, go Up → Left → Right → Down.
Try to take the Sapphire and learn the second Rocket Password. After solving the maze, you'll find the Sapphire in the center of the room. When you try to take it, however, Team Rocket will swoop in and steal it from you. During the commotion, you'll learn the second password to the Rocket Warehouse: Learn the second Rocket Password
Travel to Five (Chrono) Island. This is the location of the Rocket Warehouse, and now that you have both passwords you can get in and get your Sapphire back.
Enter the Rocket Warehouse. The Rocket Warehouse is located close to the town, and you'll need to navigate the conveyor belt maze in order to make your way through. The maze is actually pretty straightforward, and it's worth going through all of the routes to pick up the items and fight the trainers.
Get the Sapphire from Gideon. After making your way through the Team Rocket Admins, you'll finally be able to confront Gideon. After defeating his five Pokémon, he'll give you the Sapphire, which you can take back to Celio on One Island. This will allow you to trade Pokémon with Ruby, Sapphire, and Emerald.
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