Instructions
Complete every portion of the main quest up to the seventh badge you win from the gym in Mossdeep City.
Head to the Space Center, fight through several Team Magma members and speak with Steven to join him in battle against Maxie.
Head to Ever Grande City and go underwater near the city's entrance. Enter the cave to find a submarine, then surface to explore the cave. Defeat any Team Aqua members you come upon. Follow the misty path to see a large Pokemon; walk up to him to fight Archie.
Head toward Sootopolis after Steven leaves. Travel left until you hit a wall of rocks, then travel up until you can turn left again. Take this left turn and travel around the city in a clockwise motion until you reach the southern part of the city. Use your Dive ability and enter the cave on the next screen.
Save your game after entering the cave and surface to watch a cut scene of Kyogre and Groudon fighting. Speak with Steven and follow him to the Cave of Origin. Enter the cave and follow the linear path to find Wallace. Speak with Wallace, exit the cave and speak with Steven.
Use your map to return to Route 129, near Seafloor Cavern, where you fought Team Aqua earlier. Follow the linear path, fighting Trainers as you go, until you reach Route 130. Keep following the trail of trainers and you'll come upon a path between the rocks. Enter through the path to find the Sky Pillar.
Speak with Wallace and follow him to the Sky Pillar entrance. Follow the linear path up to the top of the pillar to find Rayquaza, who flies away. Follow suit and fly back to Sootopolis to see another cut scene.
Speak with Archie and Maxie, who will be blocking the gym door, and they will vanish. Speak with Steven and then Wallace. With the door unblocked, you can finally enter the gym and fight the last gym leader in the game, Juan.