Your only access in and outside Geosenge Town is by using Fly. Thankfully, the Pokemon Center is still operating. Head to the northwest exit of the town and a Team Flare Grunt will challenge you to battle.
Team Flare Grunt (Prize Money: p1,800)
Follow the path and when you're near the secret HQ's entrance, your neighbor will catch up with you and join you. Enter the elevator and activate it using the panel inside.
After exiting the elevator, you'll be in some sort of a control room. The grunts and scientists here won't fight you but you can talk with them if you wish. Go upstairs to find Lysandre. Approach him for a brief conversation and you'll have to battle him once more.
Team Flare Lysandre (Prize Money: p10,200)
Mienshao is a pure fighting Pokemon and will use Swords Dance + Acrobatics. Use flying-type moves against it to defeat it as soon as possible. Next is Gyarados. It is two levels higher when you last fought and its attacks are still the same. It's Outrage (Dragon) move still hurts very much and can easily mean defeat unless you're using a Fairy type against it. Pyroar is still the same as before; use high-tiered water or ground attacks to take it out without difficulties. Honchkrow is just an evolved form of Murkrow you fought earlier. Use Ice and Electric attacks to take it out easily.
Go past Lysandre and enter the door to the left. Continue forth and you'll be stopped by Lysandre's henchmen.
Team Flare Admin and Team Flare Grunt (Prize Money: p7,840)
After taking care of them, continue along the corridor and you'll find the next pair of Team Flare enemies upstairs.
Team Flare Admin and Team Flare Grunt (Prize Money: p7,840)
Get past the defeated opponents and continue upstairs. Shauna will join you but not in battle. Continue downstairs to fight another pair of Team Flare trainers.
Team Flare Admin and Team Flare Grunt (Prize Money: p7,840)
Continue running down the next set of stairs until you reach a large door. Shauna will help unlocking it using Clemont's device. Head inside the room and you'll have to face another batch of Team Flare members. You'll have to deal with four Admins and unfortunately, you have to talk to them individually and defeat them one by one.
Team Flare Admin (Prize Money: p3,840)
Team Flare Admin (Prize Money: p4,000)
Team Flare Admin (Prize Money: p3,840)
Team Flare Admin (Prize Money: p4,000)
Save your game and approach the tree. You'll now have to battle the Legendary Pokemon in your version of the game. pokemon x gets Xerneas while pokemon y will have Yveltal. As much most people will tell you and use the extremely rare Master Ball, I'll suggest against it. You can try your luck and use a Quick Ball at the start of the battle. Otherwise, you'll have to damage it and keep using your Ultra balls (or if you feel lucky, even ordinary PokeBalls will do). If you've done several turns already, you may also use your Timer Balls.
After capturing Xerneas/Yveltal, you'll have the option to add it to your party or not. Your friends will regroup with you as well. Shortly, Lysandre will appear and challenge you once more to a battle.
Team Flare Boss Lysandre (Prize Money: p10,600)
You can put your newly acquired legendary Pokemon to the test and let it spearhead your team in battling Lysandre's Pokemon. All of his Pokemon has grown two levels. Mienshao and Honchkrow won't pose that much of a problem if you haven't had issues dealing with them before. Pyroar can still be one-hit KO'ed by strong water/ground attacks.
Gyarados and its Outrage move can still hurt a lot. Don't bring any of your Dragons out or they'll be taken out without questions asked. The catch here is that Lysandre will use his Mega Ring and turn Gyarados into Mega Gyarados. It will change its type from Water/Flying type to Water/Dark type. Because of this transformation, your Electric attacks won't be enough to one-hit-KO it and other effective attacks like rock and ice will become ineffective. It's not all bad news though since after transforming to a Dark subtype, fighting, bug and fairy moves become effective attacks as well.
After defeating Lysandre, watch the next scenes and dialogues. You'll be back in Geosenge Town and you're free to resume your adventure with Team Flare apparently out of the way.
How do I get in there??? There is a stone rights in front of it! Why and how do I get rid of the stone?
The stone is still there but I defeated
the grunt.
but there is a stone in front of it now, so now how do I get in?