After agreeing to split up, Zinnia went alone towards Mount Chimney to summon Groudon, Leaf, May, and Norman headed towards Seafloor Cavern, Leaf's mother kept driving the car to Johto to lead Team Aqua in the wrong direction, once they would arrive, then the plan would hit the second phase.
"How come you came with me and not Zinnia?"
"She's a strong dragon type user, She can handle herself, Leaf, however, won't be able to protect himself if he's trying to synchronize with Kyogre"
"I understand, I gave my wife Slaking so if they do end up falling for the trap, she can defend herself"
"That's good, if we're lucky everything should go according to plan"
"Yes, but we should hurry anyways," He said looking down at the Pokémon they rode upon, it was a Lapras. While yes he was a Normal-type gym leader, truthfully he had a lot of other Pokémon from Johto.
"This is the place," Norman said giving a device to May and then placing another device of the same kind in his mouth and another into Leaf's"Put this in your mouth to breath underwater"The message was slightly distorted, but she got the basics placing it in her mouth as well with Norman returning Lapras to its Pokéball and diving into the ocean holding onto Leaf as he slept. They dove down into the water coming into an underwater cave where they didn't need the devices.
"Norman, did you want Leaf to return to Johto?"
"Honestly... I didn't, But you'd be surprised where Leaf gets his stubbornness from"
"I didn't take your wife as the Stubborn type"
"Nobody does until they know her, once she's made up her mind, there was no changing it" He laughed a bit.
"You seem different since the last time I saw you in Petalberg," May told him
"Oh really? Truth is I try to keep my personalities different from work and home, I didn't want to intimidate Akimaro"
"That makes sense, I've heard from my da-Professor Birch I mean, that you were once of the fiercest gym leaders."
"Well If I let Challengers just win, then they won't learn that times might get tough, you have to be sure to believe in your Pokémon"
"I see Leaf gets that from you"
"Well, truthfully, I've never seen him battle, but I've heard from Roxanne that he's strong, lacking in confidence, but resourceful. Using Mega Drain on himself to counteract the Steel-type coverage."
"His Pokémon were just as surprised as I was, It worked either way so It's still good."
It was then that something from under Leaf's glove began to shine brightly with an aquatic blue and flashing red. With every step the flashing increased until they were face to face with the great Kyogre itself, It stood before them encased in rock as Norman looked to his PokeGear on his wrist beginning to contact Zinnia
"We got Akimaro to Kyogre, are you in position?"
"Well, soon you'll be in the worst position," A deep voice said behind them, the man from Leaf's nightmares as he crushed Zinnia's PokeGear into small pieces, "After all you've done for my cause, unfortunately, you will no longer be needed" Loud pounding footsteps rushed closer with a tall, bulky man tackling into Norman causing him to drop Leaf and fall into the water, At the same time May was held back by the woman from Petalburg Woods. Leaf woke up seeing what was going on, the man from his nightmares, his father being attacked, and May being restrained, he didn't know what to do. Without thinking he tried running to save his father but was held back and in the air from his arms being locked by the man's grasp while Norman kept being knocked down and bleeding.
"S-stop it! You're hurting him!" He called out with all his might. His voice had no value, no amount of volume could stop them "T-that's enough! You have me, That's all you want!"
"Sorry shrimp, but we can't be having any interference," The man said coldly noticing the emblem shining brighter than before, with a crimson red hue.
"I said...That's enough!" He shouted with large amounts of powerful aura seeping through the glove knocking the man away and Kyogre's encasement cracking. His eyes were no longer of the kind, helpful boy Leaf was Now with Red Irises like Kyogre's, He glared towards the one attacking his father. His rage overpowered his natural sense of kindness."Get away from my dad..."He caught another punch directed toward his father casting it aside. By now Kyogre had almost been awaked, merely by Leaf's emotions, the side of him nobody ever saw.
Blinded with rage, he was quickly defeated falling unconscious by a single blow from the man. Norman himself had fallen to the same fate, May broke free from the woman's grasp shouting her friend's name and sending out her team of Pokemon.
"Oh, do you think you can stand up to me? Ha! I respect you, Lassie, not everyone can just challenge me"
"Go! Gardivoir! " May called out sending out the psychic maiden
"A Psychic-type, Ey? No problem for me, Take her down, Mightyena!" It snarled loudly once exiting the Pokéball with an aura that lowered its strength
"Use Dazzling Gleam!" May instructed as it closed its eyes, searching for the brightest part of her soul, then releasing it as a bright light of Fairy Aura.
"Quite the Punch your Pokémon has, too bad it isn't enough! Use Dark Pulse!" It was a powerful attack, leaving Gardivoir nearly unable to stand.
"Gardivoir! No!" She ran to her Pokémon in distress as she returned her friend and sending out Blaziken
"Blaziken, Not a bad choice," He said switching out for Sharpedo"Now your friend...Leaf was it? You didn't think Mega Evolution was just his thing, do you?"He asked with the Anchor necklace began to glow around where a colored stone was. As it began to shine, Sharpedo did the same, being encased with an orb made solely of power.
"Wash them all away! Use Surf!" Blaziken was quickly defeated, May was too, the tide swept her across the cavern with her Pokéballs rolling from her grasp, and within range of the man as he cracked them preventing them from being opened. May was quickly found unconscious with her last night, being her best friend being taken away.
Hours later Zinnia had run into the cavern seeing the floor of defeat, Leaf and Kyogre had been taken." Hey, Hey! Wake up!"Zinnia called out slapping both of their faces, truth is, she enjoyed slapping May's face.
"Go away..." May rolled over, she had lost her friend because she wasn't strong enough.
"You're giving up! He is your best friend, He stayed here to help the region and you're giving up on him!?"
"That was his mistake to believe in me"
"Stop acting like a Toddler! He has done so much for you, He didn't have to stay with you, he barely even wanted to go on that stupid adventure"
"How would you know?"
"Latios sensed his emotion, despite how he acted he's torn up on the inside, He stayed with you because he feared hurting others"She lifted her by the collar of her shirt" Never mind, He's in danger and you're going to be a baby about it, be my guest I'm going to go save Hoenn"She let go walking away with a Master Ball in her hand that held Groudon itself.
"Wait."
"What now"
"I'm coming with you," She ran over to Norman sending out Lapras"I need you to take him back to Littleroot," May told Lapras as it nodded, doing as told."We need to hurry, Leaf got angry, it weakened the seal"
"I know, The red orb reacted to it and it started Shining Blue, they're both in distress"
"Not just that, Kyogre's strength is his body...He's stronger than ever before, It might kill him if he uses it to wildly."
"Obviously, we need to get out of here, who knows how much damage he's done."
"Awaken Kyogre, Boy! I won't ask you again"
"N-no! I won't let you kill any other people!" Leaf cried being thrown down at the ground " I made a promise! That I wouldn't do it, I'm not breaking that promise"
"Why should you keep them safe, think about it, they don't like you, they're only pretending because they felt bad for you, to them, you're useless, nothing but a waste of space"
"Whether that be true or not... I promise I won't hurt them" He said at last.
"Heh, you ain't half-bad kid, you've got some morals all right, join us and they'll come to pass!"
"No! I already said I wouldn't!" He was determined to protect his friends, no matter what could happen to him.
"You're being really tough for me kid, you don't know your place, do ya," He asked lifting him up looking annoyed "Nevermind, you aren't worth the headache, Shelly, do as you please to the scamp"
"Right!" She said seeing him leave the room angrily, a few other grunts left as well knowing that he was nasty whenever he got annoyed. One even whispered to him before they left.
"You better watch out, with that attitude, you better be glad that we need you alive" Soon it was just Leaf and Shelly in the room.
"Sorry about his behavior, He can get aggressive at times" She admitted helping him up
"Who was that?"
"that's our leader Archie, and...Hey! What happened to that hat I gave you"
"W-well, you see, I didn't want to just wear an emblem that would associate me with...well someone who wants to flood the world"
"Well, That makes sense, but you should do this!" She looked at him with stars in her eyes with the face of a child who wanted some candy. "Pretty please? For me?" He hesitated but still declined
"Wow, almost no-one ever resists that face, you've got willpower"
Suddenly, the earth had begun to shake immensely, He fell over and so did Shelly."W-what's going o-o-on!?"
"I don't know, It's an Earthquake, you stay here, I'll go check it out"
Despite what had been at stake, He had been raised to do as told and to respect adults, He had stayed put, not just that, Norman had his Pokémon so he didn't have a way to defend himself if he got caught.
"Alright I'm back, Unfortunately, we're under attack again, so I'll have to take you with us to evacuate"Leaf knew exactly what that meant when she pulled handcuffs from behind her back. " So, You'll be our hostage until you summon Kyogre," She said it so nonchalantly, almost like she enjoyed doing that. With a single swipe to the neck, there wasn't anything stopping her from taking Leaf to awaken Kyogre.
"Shelly! You better hand him over, we both know who's stronger here"
"Oh Zinnia, you're so naive, you traitorous scum" They both glared at each other, almost like they were rivals. This, however, allowed for May to sneak past and grab Leaf without being noticed
"Have you been so busy making clothes that you didn't realize that, oh I don't know, how flooding the earth would only hurt life instead of preserving it, What happens when the world floods, There's less land for humans and our species will only create war to make the world toxic"
"What would you know about it, you're just a traitor"
"Traitor? Ha! I was never on your side, to begin with, I was just here to make sure you didn't do anything stupid, oh, and how I know?" She pulled off a glove showing the Red Orb" Because I'm Zinnia, the Lorekeeper of Sky Pillar!"She said throwing down a smoke bomb as both she and May began to run. They thought that they might get away again, fate had other plans as they were stopped in their tracks and quickly defeated by Archie
"Hey, scamps, don't you start thinking that you're better than me" Soon enough they were subdued being stuck together with chains, most likely to make sure Leaf went along with their plans.
Leaf would soon awake on Route 128 on a submarine with Zinnia and May defenseless and immobilized. Their Pokémon were stripped from them as well as Pokéballs cracked to prevent usage.
"What did you do to them!?" Leaf called out, his hands handcuffed behind his back"They have nothing to do with this, let them go!"
"Oh, but on the other hand, they'll make a good insurance policy, so awaken Kyogre, or you'll end up seeing them upon the grave." He quickly glanced towards the sealed Kyogre, then towards his friends. There was nothing to do, and no time to do it as Archie held a sword up to May's throat.
"Okay! I'll do it, I'll awaken Kyogre!" Leaf gave in, there was no way to resist. He closed his eyes, hoping to make a connection with Kyogre, in his mental state they began to make eye contact as Kyogre broke through the seal bringing upon heavy rains as well as switching Leaf's eyes into Kyogre's red. There was simply too much power for Leaf to control. So much so that the Blue orb came from his left hand and being absorbed into Kyogre's body changing its form as well as bringing deadly storms worldwide.
"N-no, this isn't what I wanted...Kyogre obey me! I am your superior!" He called out pushing Leaf aside and overboard, It was then that Kyogre, in a rage, bashed into the ship smashing it apart, It seemed like only Archie had survived, May, Zinnia, and Leaf were all lost from the world, not even they knew where they were.