And then this chapter came. It's going to continue the story and reveal some interesting things too. At least I think it will...
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Some minutes earlier

      Gladion, May, and Lisia had successfully made it out of the submarine. They saw Latios and Latias zooming off perhaps towards the Sky Pillar. (Y/n) was now gone so they must have suceeded in getting her away from the fighting legendary pokémon.

      Groudon and Kyogre were fighting dangerously close to the submarine. They had nowhere to go now that the submarine was in the middle of the sea. Gladion didn't have his pokémon with him, Ali didn't know Fly, and May didn't have a flying type pokémon since she always flew with Brendan. His bag was in (y/n) and Gladion's apartment.

      "What now?" May asked him. Before Gladion could say anything else, they heard a voice yelling at them.

        "You foolish children! This is all you fault! If you hadn't interfered with my plan, this wouldn't be happening!" It was none other than Maxie.

         "Of all the times for him to show up," Gladion complained. He was standing on the top of the submarine. How he had gotten there, nobody knew nor did they care. Maxie smirked when he saw Brendan. He knew that he had succeded in taking his life without getting his hands dirty.

        "I see you've found your friend. He isn't very useful anymore now is he?" Maxie taunted. It got to Gladion more than it got to May.

      Gladion had seen a leader of an organization go down because his beliefs were in the wrong place, but Maxie was just down right evil. "May, don't. Let me handle this one. You just get Brendan and Lisia and get out of here," he said.

        "How are we going to get anywhere there's..." she was saying but Gladion pointed up and there they were. Latios and Latias flying towards them.

      "I'll keep this psychopath busy while you guys escape," Gladion said. May carefully lifted Brendan from Gladion's back and into her arms. Latios and Latias were there just in time to get them to safety.

         Gladion was climbing up the side of the submarine and nearly slipped but he managed to get to where Maxie was just as he was yelling, "Where do you think you're going! I'm not done with you yet!" Gladion had gotten to the top completely unnoticed.

         "Hey, this is between me and you remember. They have nothing to do with it!" Gladion yelled at Maxie who turned his attention toward him.

        "So it's you? If you'd just joined me when I asked, you wouldn't have to get hurt right now," Maxie said as he pulled out a pokéball.

         "I can't battle you. I don't have any pokémon with me. Seems like we'll have to talk it out," Gladion said. He saw Latios and Latias zooming off with May, Brendan, and Lisia.

         "Who said anything about battling. You don't play by the rules, remember," Maxie said with a crazed look in his eyes. Gladion backed up a little. He was in no condition to fight off a pokémon and he didn't have (y/n) to protect him this time.

        Maxie released Mightyena who immediately charged at him and tackled him. The pokémon was trying to bite off his face but Gladion held it back by its neck and managed to throw it off of him. The Mightyena hit the submarine with a loud thud and didn't get up. Gladion turned just in time to see Crobat coming at him. He swiped at the bat pokémon as it tried to scratch at his face. It gave him some room only to use Air Cutter on him.

      He tried blocking the attack by crouching down into a ball on the ground but this only resulted in him earning several deep cuts along his back and arms. He cried out in pain as the Crobat kept attacking with the same move while Maxie stood and watched with satisfaction.

      Gladion was able to get up and jump out of the way of the Crobat's attack and then punched the annoying creature in the face.

         The moment it hit the ground Mightyena was already on Gladion's back and bit him on his shoulder causing him to fall forward. Gladion screamed out in pain as the pokémon's teeth dug into his shoulder.

      "Go for the neck," Maxie ordered Mightyena. The pokémon released its bite but Gladion used this time to flip over and send the Mightyena to the ground again. This time Gladion started to strangle the pokémon and Maxie released his next pokémon, Camerupt.

         Gladion released Mightyena in an attempt to dodge Camerupt as it charged at him but there was a small space between them. He was too late and the Camerupt sent him flying over the side of the submarine. He splashed into the cold seawater, too hurt to move as he saw a small cat-shaped thing coming towards him. It lifted him from the water with psychic powers and put him onto something that floated in the air. It was Latios.

      "You stalled him long enough, Gladion. Let's get you out of here," Latios said. Gladion held on to Latios as tightly as he could. He was in serious pain but he kept his whimpering to a low as Latios flew him to the safety of the Sky Pillar with Mew following behind.

        Once they made it there, Latios called for Latias who immediately came over to Gladion and used Heal Pulse on him which healed his wounds completely. He was getting up and asked to see (y/n) when Zinnia appeared in front of him and blocked his view.

         "You can't go over there," she said. Her voice was shaky and she looked frightened.

         "Why not," he asked as he tried to get around her but she only got in his was again. He couldn't see what was beyond the few stairs leading to the very top of the Sky Pillar.

          "Trust me, you don't want to go..." she was saying but Gladion cut her off.

      "If you don't move, I will do everything in my power to move you myself," he said. Zinnia was hesitant to move but she did anyway and said, "I warned you."

         Gladion knew that (y/n) was there waiting for him so he ran up the stairs only to find May sitting between Brendan and (y/n) with an expression that said "I have no reason to live anymore" written all over her face.

          He rushed to (y/n)'s side and asked, "W-what happened?" as he sat on his knees and pulled her limp figure to his chest.

          "Gladion. She's dead. The explosion of purple light that we saw, that was her. I don't know how it happened but when we got her from floating in the sky, she was already like that," Zinnia said as she walked towards him.

         (Y/n)'s hair had turned back to its original color, the color that it was before she broke the seal on her powers. Gladion didn't believe them so he checked her pulse but there was none.

         "No...this can't be possible. She isn't supposed to die. She can't die," he said in disbelief.

      "What do you mean she can't die?" Zinnia asked. It didn't matter if she knew so Gladion simply told her.

         "She's immoral. She isn't supposed to die. I can't lose her. I've already lost too many people I care about. I can't...I can't lose her too," Gladion said. He was trying not to cry but he couldn't help it. He pulled (y/n) into his lap and hugged her tightly. Her head was resting on his chest and he closed his eyes and rested his head on hers.

      "I'm sorry. This...this is all my fault. I shouldn't have lied to you, (y/n). I'm sorry," he whispered to her.

         "Is there anything else we can do? We have to stop this chaos or the world really will end. What are we going to do?" he heard May say as she began to panic.

         "We don't need to worry about that. There's nothing else we can do for now. I don't know anything other than how to get Rayquaza's help. Without (y/n), all hope is lost," heard Zinnia say. He didn't want to listen to this anymore. He never wanted any of this to happen.

         "(Y/n), wake up...please, I need you," he whispered. He kept holding her close and cried into her hair a little but nothing happened. The Sky Pillar was protected from Kyogre and Groudon's weather phenomena but they all couldn't stay there forever.

      Gladion felt the urge to stroke her hair and as he did this, he thought he felt (y/n) nuzzling him. He stopped crying and looked down at her to see her looking back up at him.

         "(Y/n)? You're still here. You're okay," he said as he smiled at her. The rare smile that no one ever saw. "What happened?" (y/n) asked him. "Y-you died," he said.

Some minutes later

     Gladion felt as if he was reliving everything that had happened only moments before. He couldn't find (y/n) anywhere as he rode on Latios' back. They were flying near the battle where he could only see a fallen Rayquaza and a Rayquaza twice the original's size. This one was obsidian black and had red eyes and it was beating the crap out of Groudon and Kyogre.

      Gladion didn't even care where this second Rayquaza had come from. All he wanted to do was find (y/n). The battle was nearly over as the shining black mega Rayquaza was striking the Primals with nearly fatal attacks. Gladion watched as the Rayquaza used Aurora Sphere on Groudon and then Kyogre. The two pokémon lost their primal state and fell down defeated.

      The Rayquaza roared very loudly and then it began to glow with golden light until it disappeared. That was when Gladion saw (y/n) falling from the same place that the shining Rayquaza had just been.

         "There!" he said to Latios as he pointed to where (y/n) had just fallen into the sea. Once they'd gotten close enough, Gladion jumped into the water where he'd seen her fall and swam down to save her.
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I didn't know how to make an entire chapter on shiny Rayquaza's fight against Kyogre and Groudon without making it seem a little dull so I just kinda skipped through it. Sorry...