After beating Seashore Gym. Go to Merson Backpacker's Hotel. Talk to the old man to go to the spa. Get Rock Smash and use it to get to the girls spa. Find a Go-Goggles in there. In Eaugulou City you go to the park. Go to the Cave Area to go to the desert area. Get the item by the Rock Smash rocks and give it to Sotamora in Hayward. You'll get strength. Go to Tan Boat Creek, enter the cave by surfing the lake. When you find a place that has a north cave entrance enter it. You should be in the ice cave and have 7 badges since the next part involves waterfall, find waterfall and use it to get to back cave where an important character talks about Lugia. Leave the cave and head to Botan City. Go to the building that looks like Silph Co. After talking to the man in there go to Haunted Forest and battle Team Rocket. Then go through the forest to the girl and save her from the Gengar. After going back to the Silph Co. like building go to the burial ground and talk to the ghost woman by the puddle to get a Pokeflute. You should have gotten a Bicycle from Jaeru City. Go up Cycling Road, battle Snorlax. Go through Johton Pass and when you reach the gatehouse at the end go north and you should be in Route 34. Head north to Goldenrod City and enter the orange Pokemon Center. Talk to Prof. Tim and a Rocket Grunt will appear and take the machine parts. Head back to Botan Outskirts and you can now enter the Silph Warehouse.