Giratina released a massive roar and charged at the six Pokémon opposing it. The six of them barely escaped the dangerous Phantom Force attack. Giratina vanished temporarily from their line of sight, but later reappeared on top of a nearby building and unleashed a Dragon Pulse. The six of them were cornered and were forced to counter with their own attacks. They Dragon Pulse, however, pierced straight through their attacks, successfully scattering the six of them. Ash was worried. If they couldn't break through Giratina's defense, it would be like attacking a wall. Clemont looked to Ash and recalled his Pokémon.

"We have to keep moving to make it to the gym! Giratina's distracted right now, so it's easier to sneak inside the tower! Come on!" He called out amidst the explosions going off around them. Ash refused to move.

"Clemont, I'm not leaving my Pokémon when they need me most!"

"Fine Ash, we'll think of something else. We could split up, with Bonnie and me going to Prism Tower. You can stay with your Pokémon, but please be careful. One hit from that monster and you're finished!"

"Will do. Serena! I need you to go with them! I don't want you to get hurt!"

Serena was distraught. Part of her wanted to drag Ash with them to the gym, but she knew how much his Pokémon meant to him. The other half of her wanted to stay with him. At least that way she would have assurance that he was safe. She stood there for a few seconds, before running to Ash and tightly embracing him. "Please be safe out there Ash. Come back alive." She spoke, with sadness in her voice. Ash held her tightly. "I promise." Serena let go and began to run to catch up with Clemont and Bonnie. She gave one last glance in Ash's direction before turning towards Clemont. He gave her a quizzical look, before realizing why she was upset. He put a hand on her shoulder. "He's gonna be OK. Ash isn't the type to give in so easily."

"Thanks Clemont."

"Hey you two! Hurry up! You've gotta see this!" Bonnie shouted.

The two of them caught up to her and peeked inside. Inside was Team Flare. Lots of them. Sweat started to form on Clemont's brow. This may be harder than we thought. As Serena looked inside, she saw a familiar face. Mairin? What was she doing here? Serena watched as the young girl went into a nearby room, carrying a sickly Chespin in her arms. That must be Chespie! She thought as she recalled what Mairin had said regarding her partner Pokémon. Clemont, meanwhile, had located the secret passageway that he and Bonnie had used previously, and motioned for the others to follow him down the path. "Be on your guard," he said, before entering the tower along with Serena and Bonnie.

"Sceptile, Leaf Blade! Charizard, Dragon Tail! Greninja! Water Shuriken!"

"Sceptile!"

"CHARIZARDDD!"

"Ninjaaaa!"

The three Pokémon attacked Giratina, each of them proving how much they had improved since he last saw them. Giratina dodged them effortlessly, and countered with his own Dragon Pulse. The attack struck the three full on, causing them to flinch. Seeing this, Ash released Goodra, Snorlax and Noivern.

"Goodra! Dragon Pulse! Snorlax! Defense Curl! Noivern! Dragon Claw!"

Each of the Pokémon did as they were told, and fired off their attacks at the legendary. The attacks were deflected with several rapid Shadow Balls. Noivern, however, managed to land a solid hit on it with Dragon Claw. Giratina slid back a bit, and roared, enraged by the pain Noivern caused. Ash continued to command the six Pokémon, but Giratina, although slower than before because of the damage inflicted on it, continued to dodge the oncoming barrage of attacks. It then prepared to use Phantom Force once again, when Ash noticed something. Whenever it used the move, a shadow appeared roughly in the same area as to where it would teleport to. With this in mind, he ordered Greninja to gain altitude, while the others distracted the Legendary with their attacks. Charizard was eager to take down Giratina and lunged at it with a Slash attack. Giratina swiftly cancelled its attack and dodged, before it attacked with Dragon Pulse. Charizard fell to its knees, struggling to get up. As Giratina was about to finish it off, it was tackled by Snorlax. Meanwhile, Sceptile appeared from its hiding spot and jumped onto Giratina's back. It then slashed at it with Leaf Blade. Giratina howled in pain, before flinging Sceptile into a nearby building. Ash grit his teeth. Why wasn't it using Phantom Force? For his plan to work, he needed it to use Phantom Force. Noivern took off into the air and fired off a supersonic attack. Giratina was struck in the head by the attack, successfully confusing it. It then used Phantom Force. Ash signaled to the others to break off their attacks. Giratina fell for the trap and aimed directly for Goodra. As it executed the move, however, Greninja appeared suddenly and leaped from its perch. Giratina reappeared from teleporting and was met with a Super Effective Ice Punch to the face. It slumped down in front of Greninja and the others. Charizard then unleashed a deadly flamethrower on it. Giratina collapsed, unable to take any more hits. Ash could see it could still fight, but also knew it was too weak to put up much of a fight, he recalled his Pokémon and ran as fast as he could to Prism Tower. As he passed Giratina however, the draconic Pokémon fired off a final Shadow Ball at Ash, before it fainted. Ash turned at the sudden noise and was struck in the chest by the attack. As his consciousness was leaving him, he told Pikachu to let out as many of his Pokémon as it could and warn Clemont and Serena. He then blacked out.

When Ash came to, he saw that he was suspended in front of Prism Tower and was restrained by unusual floating binders. He looked around and saw his Greninja next to him. "Greninja! What happened?" he asked groggily.

"Ninja," the ninja frog Pokémon responded.

"So you're finally awake Ketchum."

Ash turned, and was shocked at the sight of another familiar face standing in front of him. "Lysandre? What are you doing here? It's dangerous," Ash said. Lysandre just grinned.

"Ash, I'm disappointed at your naivety. Did you really think I was interested in you Greninja because it could be used to help demonstrate the bond of Pokémon and trainers? The energy required to cause such a transformation could be useful to Team Flare's cause, you must understand that right? I am Team Flare's leader."

Ash was shocked, but was quick to leer at Lysandre. "You won't get away with this!"

"Oh? Let me introduce you to the energy extractor we have invented. When used, it drains all the energy that is used to form Mega Evolution, or in your case, Synchro-Evolution."

Two robotic insects flew up to where Ash and Greninja were suspended.

"Still think I won't get away with it? Fire," Lysandre ordered coldly. The two robots unleashed a powerful beam that to Greninja, felt like the strongest Drain Punch possible. To Ash, the excruciating pain caused him to scream out. Greninja cried out to its trainer, but Ash knew he couldn't help his friend.

"I'm sorry… Greninja….."

Lysandre smirked as the energy extractor finished the task it was given. Ash was now under his control, and Greninja couldn't synchronize with him because it had fainted in the process.

"We have finally obtained enough energy to power the Ultimate Weapon, thanks to Ash and his Greninja, as well as Alain's blind obedience. Soon, we will finally fulfill our dream." As he was speaking, he noticed a person approaching from the corner of his eye. He turned and saw an enraged Alain.

"WHAT HAVE YOU DONE?!" he shouted.

Lysandre cursed under his breath and commanded Ash to attack Alain. Alain was surprised when Ash started to walk forward and remove the one Pokeball that Lysandre allowed him to keep. He released Infernape, who was also under the mind control, and commanded it to use a Fire Punch on Alain. Alain executed a backflip and successfully evaded the attack. He then released his Charizard and Mega-Evolved it.

"Keystone, respond to my heart. Beyond evolution, Mega Evolve!" Alain said before turning to face Lysandre with an icy glare. "I trusted you. I collected Mega Evolution energy for you day in and day out. I helped to further your research. I collected your own Mega Stone as well as many others for you. How could you do this to me?!"

"You are truly a pathetic, Alain. Look around. What do you see? Destruction. Chaos. Pain. Such is the will of Team Flare. You caused all of this by blindly following me, and now you will be erased from existence along with all the pitiful humans of this world!"

Alain's eyes widened. He caused all of this chaos by collecting Mega Evolution energy for Lysandre, thinking that it would save Mairin's Chespin. Alain pounded his fist into the wall repeatedly. "No, no, NO! What have I done?!" Alain looked up and saw Lysandre order Ash to attack once again. Mindlessly, Ash proceeded to attack Alain with his Infernape. Alain tried to snap Ash out of it, but ultimately failed to do so. "Infernape! Thunder Punch on Charizard!"

"Counter with Dragon Claw!"

Infernape lunged at Charizard and attacked it with a flurry of punches. Charizard was forced on the defensive, and countered with Dragon Claw. As it let its guard down to catch a breath, Infernape slammed its fist, crackling with electricity, into Charizard's chest. Charizard stumbled backwards, but stood strong.

"Ash snap out of it!"

Clemont and the others had made it into the gym undetected. As they made their way into the gym, they looked around. One side of the gym's wall had crumbled from when Z2 had used Land's Wrath earlier, and a Mega Evolution cannon was protruding out of the cavity. Clemont headed for the cannon's controls, followed by Bonnie and Serena, but when Bonnie peeked into the next room, she was terrified. Inside the room was Squishy. He was being put under the control of Team Flare and forced to fuse with Z2, who was already controlled. Meanwhile, Clemont reached the cannon and Serena looked around to see if anyone was there. When she heard an explosion from above, she looked up and the sight she beheld froze her. There was Ash, his body glowing red, attacking Alain mindlessly with Infernape. Just then Pikachu and the others rushed into the room and collapsed. Pikachu tried to explain to Clemont what happened, but he couldn't understand what was going on. He glanced at Serena, who pointed to the sky. Clemont was shocked to see a controlled Ash carrying out Lysandre's orders like a robot. Before he had time to act, the alarm went off. Grunts were sent in and Clemont was surrounded. Serena had run off after Ash, and Bonnie was still inside the room holding Squishy. Pikachu and the other Pokémon ran in front of Clemont, while he released Chespin Luxray and Bunnelby. Clemont continued to get to the cannon's controls. Pikachu and the others held off the incoming waves of enemies, and Clembot, who was in sleep mode, awakened and released Heliolisk and Magnemite. All of them grew weary, but continued to hold off the attacks. Clemont then ordered Electric Terrain to be used, and Luxray successfully electrocuted the grunts. Snorlax then used Rock Slide and blocked the entryway, preventing any more from coming. Clemont ran over to the computer controls, and obtained a map that showed where the remaining cannons were stationed. After getting the important information from the computer, he had Heliolisk use Thunderbolt. The mind control beam controlling Dialga and Palkia was disabled, causing the two of them to return to normal. Hoopa was enraged at the two turncoat Pokémon, and engaged the two in combat. Meanwhile, Xerneas and Diancie had reached Prism Tower, when they heard the cry of a familiar enemy. Yveltal had arrived.

"Ash, snap out of it please!" Serena cried.

"GET AWAY FROM ME!" Ash shouted back. Infernape readied a Mach Punch and lunged at Serena. The attack was deflected away by Charizard's Dragon Claw.

"Get behind me Serena!" Alain ordered.

"But Ash—"

"But Ash can't hear you! Get to him as soon as we take care of Infernape!"

Charizard readied a Flamethrower, and struck Infernape in the chest. Infernape slid backwards, but countered with a Thunder Punch. Charizard reeled backwards from the super effective hit. Meanwhile Lysandre intensified mind control on Ash. His eyes grew red and he had Infernape attack Alain, once again with a Flame Wheel. Alain evaded, and then realized something. If they could destroy the controller, Ash would be free from Lysandre's control. If he was freed, Lysandre's plan would be foiled. Lysandre realized this, and frantically released Gyarados to end Ash's life.

Meanwhile, Serena rushed over to Ash and tried to snap him out of it. "Hang in there Ash! I know you're strong. You can fight it!"

"Get out of my head!" Ash cried, trying to resist the mind control.

"Gyarados, Hyper Beam on the boy!" Lysandre shouted.

"Ash!" Serena ran over to him as quickly as she could. She tackled him out of the way and was skimmed by the powerful attack. Serena screamed in pain and fell to her knees. Alain quickly used the smoke caused by the explosion to destroy the mind control device that was possessing Ash.

"Ughh—my head…. Where am I? What happened Infernape?"

Infernape was just as confused. Ash took the time to look around him. He noticed Alain's Charizard was locked in combat with Lysandre's Gyarados. He then saw Serena, slumped on the ground near him.

"Serena!" Ash called out, running towards her limp figure. He lifted her into a sitting position. "Serena! Can you hear me!" he called out. Suddenly a thought entered his mind. A thought that haunted him. Serena wasn't waking up. What if she never woke up? Ash crumpled on the floor, bringing her body in a tight embrace. "Serena…" Ash cried. Just then, Serena stirred. She opened her eyes and saw Ash crying next to her.

"Ash…?" she uttered weakly.

"Serena! You're OK!" Ash said as he tightly embraced her. Serena hugged him back.

"I'm—I'm glad you're OK Ash," she spoke quietly.

"Me too Serena. But what happened to you?!"

"I—I took a hit t-that was aimed for y-you…" she said softly. Serena's embrace on Ash weakened, before she slumped down and panted heavily.

"We need Brock to have a look at you."

Serena agreed, and the two fled to the Pokémon Center.