In the underground chamber of Team Flare's Secret HQ, AZ gasps in shock as Xerneas states telepathically that a human shall hold it inside a Pokéball. He wants to know if it plans to voluntarily join a trainer's party as a team member, but the giant deer ignores the question, and simply says they should get outside. It instructs AZ to get the fainted kids onto its back, and the giant man gently picks up an unconscious Clemont and Emma with his big hands. However, they are soon intercepted by Xerosic, who attacks with Malamar and refuses to let them go.

AZ decides to stay behind and fight, and tells Xerneas to leave with the kids first. Xerneas steals a look at Trevor, Tierno and Shauna who have also fainted on the midair platform, and takes a great leap, knocking them off the platform onto its own back before breaking out through the ceiling of the chamber. Xerosic grits his teeth in anger, but soon hears the voice of Lysandre, who tells him not to fret. Xerosic is glad to see that his Boss is fine, although his cybernetic suit is gone and Gyarados has reverted back to its usual state. Lysandre grins that the entire Kalos has already been swept by the Ultimate Weapon, and there is nothing that Xerneas can do on its own.

Above ground, Bryony turns off the propellers from her boots and lands with a smile as she marvels at the fully blossomed Ultimate Weapon, which she calls the beautiful poisonous flower. Earlier, although she has failed to stop the kids from getting underground, she didn't attempt to pursue because she felt that their odds of thwarting the weapon from activating was extremely low. The fact that the Ultimate Weapon successfully fired proved that she was right. She assembles the Team Flare Grunts of Team A, and orders them to contact their spying team across to region to report on the purification status. She can see that neither of them has been hurt by the weapon's deadly beams, and thinks it is clear that the 5 million they paid for their suit was worth it.

At that moment, Y speaks up, and realizes that the red suits have protective functions after all. She climbs back onto her feet, and mocks that Team Flare's so called 'chosen ones' are nothing but people who could afford to pay and join the organization, which is certainly an absurd criteria of selection. Bryony is irritated by her words, and argues that there is nothing wrong with the notion. She hollers that those with wealth are naturally the ones who get to pick a future they deem best, but on another thought, decides that it is not the time to debate on the topic, since the more important question is how Y managed to stay alive.

Y reveals that Olympia and Valerie's Pokémon have shielded them with their psychic powers, and Bryony discovers with astonishment that the Gymleaders have been unharmed as well. She finds it hard to believe since shields as such shouldn't be able to withstand the explosive waves given off by the weapon's full activation, let alone the actual beams of destruction from it. She demands to know what they have done, and Y barks that she has no idea what she is talking about. With that, the girl sends out Rhyrhy to attack, and Bryony quickly defends with Bisharp. She believes that something out of her calculations must have occurred to result in this situation, and tries to figure out what it could be. Valerie and the other Gymleaders decide to join in the fight, but suddenly feel the ground shaking beneath the feet. Grant wonders if it is yet another enemy, and soon, Xerneas breaks out from the ground, causing everyone to gasp in bewilderment.

Down in the underground chamber, Malamar and Pyroar have successfully seized AZ. Xerosic checks on the computer, and starts to get reports from their spying team everywhere. However, the results stun him, and Lysandre wants to know what it is. Feeling anxious, Xerosic reports that he has received status updates from Route 10, Route 11, Route 12, Shalour, Anistar, Coumarine, Cyllage and the Parfum Palace, all of which have suffered damage from the Ultimate Weapon's beams. Yet, the total count of humans and Pokémon who have been purified by the weapon so far is zero, and the results cause Lysandre to exclaim with disbelief.

AZ remarks that there are several reasons why things didn't happen as Lysandre had hoped. First, he launched the weapon when it was only 70% filled with bioenergy. Second, when Xerneas reverted back from its Tree forme, the bioenergy back-flowed into it, further draining power from the weapon. Third, due to the repression from the Gymleaders, the weapon was fired at a time it didn't fully blossom. Also, although it was only barely in time, the kids did manage to pull out the Key. In other words, thanks to the combined efforts of resistance from those Lysandre insulted as weak beings only meant to be 'taken' from, his scheme has been foiled.

Lysandre stays silent for a moment, and finds it shameful that such words should come out from the mouth of a man who dominated Kalos like a king 3000 years ago. AZ lets out a snicker, and counters that this man he spoke of shall side with and share the fate of the weak beings of Kalos he planned to purify. Lysandre sighs and states that he was actually hoping to work together with AZ, but AZ rejects the offer by calling it wishful thinking. Lysandre gets irritated by AZ's attitude, and barks that his heart is simply too weak to fulfill such a great cause.

Back above ground, Y and the Gymleaders watch with surprise as Xerneas crouches down to let off the unconscious kids from its back, who slowly come around as they hit the floor. Bryony learns of what has happened from Xerosic via her communication device, and feels upset that she has miscalculated things after all, which resulted in their low odds of success. Trevor groggily gazes at his surroundings and wonders where he is, and jumps with bewilderment when he realizes that Xerneas is right next to him. X, who has also regained consciousness, tells Trevor to be quiet, and points out that Xerneas is currently seeking out the person who shall command it.

Everyone gasps at X's remark, and sees that the legendary Pokémon is indeed darting its gaze back and forth between all the humans at the scene. X explains that although he was only semi conscious, he heard Xerneas talking about entering the Pokéball of a human just before they left the underground. Y is thrilled that Xerneas is taking their side, but X doesn't get her logic, and says it simply means Xerneas wants to protect Kalos from destruction. Y argues that it is essentially the same thing, and decides to try her chance by taking out an empty Pokéball. However, another ball gets thrown at Xerneas at that moment, which the giant deer fends off with its antlers. Y turns around to discover that it was Bryony who made the attempt, and the green-haired Scientist grins that she shall recapture Xerneas to raise their odds of winning again. She gestures to Bisharp and the Grunts of Team A, and orders them to weaken Xerneas to aid its capture. With that, the Team Flare Grunts send out a Mightyena, several Liepards, Scraftys and Swalots, and get ready to attack.

Y tells her friends that they have no time to waste, and Shauna wants to know what she plans to do. Y states that Xerneas has already expressed its wish to work with humans, and she sees no reason to sit back and wait for its decision. Rather, they should grab the chance to command Xerneas proactively and fight Team Flare. Shauna thinks Y is talking nonsense since Xerneas may have its own idea, but Y feels confident and believes that a positive response from Xerneas will imply that it has chosen that person as its trainer. Trevor still has reservations about the idea since they don't know what moves Xerneas can use, but Y declares that she does and takes a leap towards Xerneas. Wearing a look of determination, she urges the legendary deer to acknowledge her words, and proceeds to command a Geomancy. In the next instant, beams of seven-coloured light pour out from the ground and get absorbed into Xerneas's body, turning its antlers a shade of gold as jewel-like protrusion spurt from them. Bryony gasps that it has entered its Active Mode, and Y follows up with a Horn Leech. Without hesitation, Xerneas swings its giant antlers towards Bryony, the Team Flare Grunts and their Pokémon, and with a sweeping motion, hurls them all into the air, causing them to crash and faint.

Shauna exclaims in shock and confusion at what has just happened, and X shows her the magazine clippings from the Lumiose Journal 3 years ago which Alexa gave them. Shauna sees that the article is on Xerneas and starts reading out loud, but Y interrupts and recites the passage from memory:

'Xerneas, the Pokémon that 'gives', has none but one single time when itself is 'given'. Using a move that unleashes seven-coloured lights, it draws energy from the land to heighten its own powers, which people in the past unanimously called Geomancy.'

Shauna bolts in bewilderment that Y has memorized the line, and Tierno is apparently taken by surprise as well. Trevor wonders where she learnt of Horn Leech since it was not mentioned in the clippings, and Y explains that they have seen it use the move while fighting Yveltal in Vaniville. She then hovers towards Xerneas to pat it on the head, and expresses her gratitude to it. She decides to nickname it Xerxer, and hopes that they will work together from now on.

When Trevor would think back on this moment many years later, he would always remember how shocked he was that Y managed to learn so many things from reading the journal entries of Alexa. After all, he himself and everyone else were only focused on finding out why they lost their hometown and what Team Flare's true intention was all this time.

Y turns her attention to the Ultimate Weapon, and thinks their next task is to destroy it before the enemy tries to pull off what they did a second time. However, a voice comes on from above to challenge whether she can really succeed, and everyone looks up in bewilderment to see Malva riding on a giant black and red bird. Malva towers over the kids, and voices out her surprise that not only did the Ultimate Weapon failed to fire but Xerneas has been taken as well. Tierno gasps that the black and red bird is no other than Yveltal, and Shauna also points out that the pink-haired woman is the TV reporter who took away Diantha. Malva wastes no time in ordering Yveltal to fight and defend the Ultimate Weapon, and Y quickly responds by commanding Xerneas forward. Yveltal's claws clash furiously with Xerneas's antlers, and Trevor is bewildered that he is witnessing a battle between the two creatures a second time. The only difference is that Xerneas is fighting under Y's command this time, and Yveltal under Team Flare's Malva.

Y demands to know what happened to Diantha, and Malva giggles at the question. She wonders if Y is aware of the reason she went underground in Route 8's forest, and with a grin, reveals that the dormant 'Cocoon' forme which Yveltal has retreated to was actually resting directly below the 'Tree' forme Xerneas has become. Everyone bolts in shock at Malva's words, and the pink-haired woman teases them to make a wild guess at what happened to Diantha if she ends up being the one successfully capturing Yveltal. She then decides to clean things up, and gets ready to order an Oblivion Wing from Yveltal. However, she is interrupted by Xerosic, who has left the underground and gone airborne by boot-propellers with Mable and Aliana, the latter two supporting an unconscious Bryony between them. Xerosic states that the Boss has ordered a temporary retreat, and Aliana giggles that since Yveltal and Xerneas are equal in strength, there will be no way to stop their battle if they begin to fight. Mable states that the two legendary creatures should be self conscious about the endless war, and Xerosic steals a look at Y, wondering if their human trainers have the physical capabilities to stand up to such a long battle.

Y turns to Xerneas to confirm that what the Team Flare Scientists said is true, and the giant deer decides that retreating may the best move at the moment. It gets everyone to cling on to it, and after surrounding itself with a bright light, leaps into the skies and flies off into the distance.

Nearby, at the entrance of Geosenge, a caped solitary figure accompanied by his Charizard stands under the stone arch. He watches the legendary Pokémon fly away, and muses over the claim that there are no ways stop a battle between Xerneas and Yveltal. The truth is, there is actually a method, since in addition to X and Y, there is also Z, provided that it truly exists…