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After defeating Wulfric, you hear from Tierno that Lumiose City is finally open again. You go there and are direct to go straight to Sycamore's Lab. (Bonnie tells you her Clemont is checking the Power Plant one last time, just to be safe). There, you speak to Sycamore for a bit about Zygarde before Lysandre invites you (and only you) to the Flare Cafe. At the Cafe, Lysandre invites you to join Team Flare, though the game won't actually let you. He then challenges you to stand against Team Flare if you think you can handle them. While you are battling Team Flare in the hideout, Lysandre attacks the lab and steals the other Zygarde Core, taking it to Geosenge Town where the Ultimate Weapon is raised up, being powered up by Xerneas and Yveltal. Heading into the base, before you can free the Legendary Pokémon, the Zygarde Core that Lysandre stole and brainwashed appears and immediately attains its 50% form. Like in XY, you must catch this Zygarde to continue.
If you have obtained all 50 Zygarde Cells (including the Core you caught) before catching the 50% Zygarde in Team Flare's Hideout, you can have a 50% Zygarde yourself. With both 50% Zygarde, if you have a 50% Zygarde in your party when you face Lysandre for the last time, you automatically open with Zygarde and it immediately attains it's 100% form. After defeating Lysandre, he tries to blow up the base with you in it, but Zygarde repels the attack, saving the base and making Lysandre get caught by the police. (If you don't have Zygarde in your party for the battle with Lysandre, Zygarde appears from the Zygarde Cube instead, since you have at least a 50% Zygarde).
After this, the plot plays out the same as XY, except Clemont is the last Gym Leader. He has a Mega Ampharos. After you beat him, he gives you a special Electro-Glider that blasts you up into the air and lets you Soar across Kalos.
