After you defeat the Pokémon League Champion for the first time, the Delta Episode will begin the next time you open your game.
Get the Tickets
After the cut scene that starts the Delta Episode, you will be in your room in Littleroot Town. Go downstairs. You will get the tickets to the star show in Mossdeep Space Center, and your Dad asks you to invite your neighbor. Go outside.
Visit Your Neighbor
Outside your house, you find Zinnia, whom you saw in the cut scene that started the Delta Episode.
After she leaves, go next door. You find out that Zinnia stole your neighbor's Key Stone, so your neighbor can no longer use Mega Evolution, but now Zinnia can.... Your neighbor says that Zinnia said that she will go to Petalburg next. Go to Petalburg now.
Help Wally in Petalburg
Go to Wally's house, which is next to the Gym. The Team Magma/Aqua Admin is demanding that Wally give up his Key Stone. You'll have to battle the Admin to put a stop to this. After you defeat the Admin, you find out that Wally's Key Stone is missing.
Afterward, you get a call from Steven, asking you to visit him at the Devon Corporation in Rustboro.
Meet with Steven at Devon Corp
Steven will be standing outside the Devon Corporation building in Rustboro. Inside, Mr. Stone asks if you are ready to listen to his long story. If not, you can say no and talk to him later. Otherwise, say yes. During the long story, Mr. Stone asks you to go to Granite Cave to find the Meteorite Shard that they need.
Get the Shard in Granite Cave
Go to Granite Cave. You can Fly there directly. Go into the cave, and go to the room with the cave paintings, where you met Steven earlier in the game.
You find Zinnia. She wants to battle you, but first she asks if you are ready. If not, you can say no and then leave the cave to prepare. Otherwise, say yes and the battle will start. Zinnia has a level 55 Tyrantrum, a level 55 Altaria, and a level 57 Salamence.
After you defeat her, you get a Meteorite Shard.
After that, Steven asks you to come to the Mossdeep Space Center, so go there now.
Learn about the Meteorite Plan at Mossdeep Space Center
Go inside and talk to the girl in the northeast corner of the building.
After a cut scene, Zinnia asks if you have a better plan. You can answer however you want.
After that, put a pokémon in your party that knows Waterfall, then go to Meteor Falls whenever you are ready. You can Fly there directly.
Visit the Back Room of Meteor Falls
You will need to bring a pokémon that knows Waterfall. Go into Meteor Falls and use waterfall to go up the big waterfall in the main room. Go into the door at the top. Steven is in the back of this room, but you can't go there directly. From where you entered, go northeast and go down the ladder that you find there.
From there, go southwest, then west, then north. You'll have to battle a Dragon Tamer. Go north and go up the ladder that you find.
Go east and have a Double Battle with the Old Couple, then go up the stairs to the right of them.
Steven is near the top of the stairs in this room at the top of the waterfall of Meteor Falls, so go talk to him.
After the cut scene, you can use an Escape Rope to leave, if you have one, or walk south from the old lady, then go southwest and go through the door to return to the top of the waterfall in the first room of Meteor Falls. Go down the waterfall, then go up the stairs to the right and cross the bridge to reach the exit.
Your next destination is the Devon Corporation building Rustboro City.
Deal with Trouble at Devon Corp
When you approach the door of Devon Corporation, a cut scene starts. You will have to battle a Grunt, and then another Grunt, and then another.
Afterward, the scientist says to follow the thieves to Mossdeep Space Center.
Do Battle at Mossdeep Space Center
In Mossdeep, approach the Space Center and you will find the Team Magma/Aqua Admin and some Grunts. Go into the Space Center and go to the stairs that you went up earlier. You will have to battle five Grunts at once in a Horde Battle.
Afterward, go upstairs. Steven will ask you to battle alongside him against the Admin. If you're not ready, say no, then prepare. If you are ready, say yes. You and Steven will have a Double Battle against the Admin and a Grunt.
Watch the cut scene after the battle. You can answer Zinnia however you wish.
Your next destination is the Team Magma/Aqua Hideout in Lilycove City.
Visit the Team Magma/Aqua Hideout
Go into the hideout, past the Grunts. Step on the northernmost warp spot. Then go down the stairs in the northern corner. You will have to battle Grunts as you go along.
Go to the southern corner of this area and step on the warp spot there. Follow the southern path (south of the lab) to reach the next warp spot in the northern corner. Then in the next room, step on the southern warp spot.
First, step on the right or left warp tile to go to the next row. Then step on the middle warp tile to go to the next row. Then step on the warp tile on the right (in Omega Ruby) or left (in Alpha Sapphire) to go to the next row. Finally, go around the middle tile and step on the far one to go to the next area.
Go up and watch the cut scene. You will get a Mega Stone. Afterward, Steven calls and asks you to meet with him in the second floor of the Mossdeep Space Center.
You can get the items from the corner of this room now if you didn't before. There is a Master Ball, some Electrodes, and a Nugget.
You can't use an Escape Rope here, so go back to the room with the many tiles and step on the middle tile, then step on the left or right tile, then step on the northern tile. Go north and step on the tile there, then step on the tile in the southern corner. Go up the stairs in the next room, then step on the tile in the northern corner. Then you can go south to leave the hideout.
Regroup at Mossdeep Space Center
Go up to the second floor of the Mossdeep Space Center again. Steven will ask you if you remember Wallace from Sootopolis City. He's the eighth Gym Leader. After the cut scene, go to the Cave of Origin in Sootopolis City.
Visit Wallace at the Cave of Origin
In Sootopolis City, Surf to the west side, then go up the path that goes along the east side of the Poké Mart. Go northeast, then go southeast down the stars. Approach the bridge to the east. Cross it and you find Wallace. He says to go to the Sky Pillar when you're ready. It can be reached from Route 131.
Reach the Sky Pillar in Route 131
You can only reach Route 131 from the east. If you have never been there before, Fly to Route 128, then Surf South to Route 129, west to Route 130, and west to Route 131.
Surf to the north part of Route 131 and you will find Wallace at the entrance of the Sky Pillar. Before you can go in, you must battle Wallace. He has a level 55 Wailord, a level 55 Tentacruel, a level 55 Ludicolo, a level 55 Whiscash, a level 55 Gyarados, and a level 57 Milotic.
After you defeat Wallace, you can enter the cave. Go through the cave to reach the top of the cliff, then go north into the Sky Pillar. After you have gone in, you can Fly back here any time.