The Team Flare Secret HQ (Japanese: フレア団秘密基地Team Flare Secret Base) is a facility located underneath Geosenge Town, serving as the main base of operations and headquarters for Team Flare.
The facility is constructed around and inside the ultimate weapon from ancient Kalos. Although the secret entrance to the base can be found at the northwest corner of Geosenge Town when the player first visits the town, it cannot be identified as such and thus used to access the facility until the ultimate weapon has been remotely activated from Lysandre Labs. After Lysandre is defeated for the final time, the base is destroyed, rendering it inaccessible.
In Dancing Vivillon, it was revealed that Team Flare had taken Clemont hostage at their HQ after his disappearance near Camphrier Town. After Clemont regained consciousness, Xerosic forced him to start building a machine for Team Flare. With the help of a wild Klefki, Clemont was able to inform X and his friends of Team Flare's base's location in Geosenge Town. The group, alongside with Emma, subsequently stormed the base, while the Kalos Gym Leaders worked above the ground to prevent the ultimate weapon from opening. Through a warp tile, X was accidentally transferred to the ultimate weapon's control room, where came face to face with Lysandre. While X and Lysandre started battling, Emma came across AZ, imprisoned in a cell.
Using the Key Stone that Celosia had previously stolen from Korrina, Lysandre was able to Mega Evolve his Gyarados. Although X fought hard, he was eventually defeated by the Team Flare Boss. During the battle, however, Xerneas woke up, taking back most of its energy absorbed by the ultimate weapon. Despite this, Lysandre still decided to fire the weapon. Although the weapon was successfully fired, X and his friends' interference weakened its blast enough so that no innocent lives were taken. With their big plan foiled, Team Flare subsequently abandoned their HQ and went to hiding in the Pokémon Village.
Because XerneasX/YveltalY must be captured in order to progress the plot, the 31st Box in the Pokémon Storage System will not become available until then. This is so that they are caught even if at that point, the player has a full party, reached the normal limit of 30 Boxes, and filled each one with Pokémon.
Much like the events of Pokémon Black and White, if the player's party is full, the caught Legendary Pokémon can be immediately added to the party from the PC by sending another party member to the PC.