After the Ultimate Weapon is activated in Geosenge Town, head northwest into Team Flare Secret HQ to stop them.
Go Below
When you go through the door of the stone hut, you enter an elevator. Check on the buttons in the middle to activate the elevator and go down. Then go through the door.
You can talk to the Grunts and researchers. They won't battle you. From them, you can learn more about what's going on.
If you're ready for battle, approach the stairs up above.
Battle Lysandre
After you enter Team Flare Secret HQ, go north and you will have to battle Lysandre again. He has a level 47 Mienshao, a level 47 Honchkrow, a level 49 Pyroar, and a level 51 Gyarados.
The Mienshao is weak to Flying, Psychic, and Fairy moves. It uses Fighting and Flying attacks, and it also has the Swords Dance move, which increases its Attack.
The Honchkrow is weak to Rock, Electric, Ice, and Fairy moves. It uses Dark, Flying, Normal, and Steel attacks.
The Pyroar is weak to Fighting, Ground, Rock, and Water moves. It uses Normal, Fire, and Dark attacks.
The Gyarados is very weak to Electric moves, and is weak to Rock moves. It uses Water, Ground, Steel, and Dragon attacks.
Find the Legendary Pokémon
After the battle, if you want to heal, you can go to the Pokémon Center. Otherwise, go west from Lysandre and down the stairs.
There are no items in this area. You'll just be battling your way to the Legendary Pokémon. Your neighbor will fight alongside you in the double battles that you will face here. He has a level 45 Meowstic, a level 49 starter that is strong against your starter, a level 46 evolution of Eevee (Jolteon if you chose Chespin, Flareon if you chose Fennekin, or Vaporeon if you chose Froakie), and a level 46 Absol.
The first battle is against a Team Flare Admin and Team Flare Grunt who have a level 50 Toxicroak and a level 48 Liepard.
Feel free to go back to the Pokémon Center after each battle
Next, you battle a Team Flare Admin and a Team Flare Grunt who have a level 50 Manectric and a level 48 Mightyena.
As you proceed, Shauna will arrive, and your neighbor will agree that you should stick together.
After that, you fight a Team Flare Admin and a Team Flare Grunt who have a level 50 Houndoom and a level 48 Scrafty.
Keep going and you will reach the door to the chamber where the Legendary Pokémon of Kalos is being drained of its energy to power the Ultimate Weapon. Shauna unlocks the door.
At this point, you are free to leave and prepare if you wish. When you're ready, go through the door.
Before you can free the Legendary Pokémon, you have to defeat all four of the Team Flare Admins in the room. You can leave the room at any time between battles, so feel free to go all the way back to the Pokémon Center if you want to.The female Team Flare Admin on the left has a level 50 Swalot.
The female Team Flare Admin in the front middle has a level 47 Liepard and a level 48 Manectric.
The male Team Flare Admin on the right has a level 47 Mightyena and a level 48 Houndoom.
The male Team Flare Admin directly in front of the machine has a level 50 Golbat.
Catch the Legendary Pokémon
After this, it's time to catch the Legendary Pokémon of Kalos! If you are playing Pokémon X, you will face Xerneas. If you are playing Y, you will face Yveltal.
Walk up to the machine, and the legendary Pokémon will hatch.
Don't use your Master Ball!! If you knock out the legendary Pokémon, it will just get back up and you have to try again. There is no risk of losing the legendary Pokémon, so you should save your Master Ball for more difficult-to-catch legendaries later in the game.
At the start of the battle, before you make any moves, try throwing a Quick Ball. You might get lucky and catch the legendary pokémon right away. If not, then to have the best chance of successfully catching the legendary Pokémon, lower its HP as much as possible, using False Swipe if you have it. Then inflict Sleep or Freeze on the legendary Pokémon. After that, start throwing Dusk Balls, or Ultra Balls if you don't have any Dusk Balls. If the battle goes on for a long time, start throwing Timer Balls.
Battle
After you catch the Legendary Pokémon, you can add it to your party from the PC Box if you wish. You will have to put one of the pokémon from your party into the PC Box to make room for the legendary pokémon.
After this, you have to fight Lysandre once more. He has a level 49 Mienshao, a level 49 Honchkrow, a level 51 Pyroar, and a level 53 Mega Gyarados.
The Mienshao is weak to Flying, Psychic, and Fairy moves. It uses Fighting and Flying attacks, and it also has the Swords Dance move, which increases its Attack.
The Honchkrow is weak to Rock, Electric, Ice, and Fairy moves. It uses Dark, Flying, Normal, and Steel attacks.
The Pyroar is weak to Fighting, Ground, Rock, and Water moves. It uses Normal, Fire, and Dark attacks.
The Mega Gyarados is weak to Fighting, Bug, Grass, Electric, and Fairy attacks. It uses Water, Ground, Steel, and Dragon attacks.
Continue on your Journey
After it's all over, Shauna says you should go back to Anistar City to resume your journey. After you get there, you should go east from the Pokémon Center. You'll get a Holo Clip from Professor Sycamore asking you to meet him in Couriway Town. Keep going east, then south, to reach Route 18: Vallée Étroite Way.