Weather Trio

It seemed like it would be a normal day for the gang; they were on a ferry heading towards Mossdeep City. But they were being followed by Team Rocket. Jessie, James and Meowth made another attempt to steal the gang's Pokemon and they were sent flying. But in the process the gang fell overboard and landed in the ocean. Tomo quickly returned his Growlithe so it wouldn't get wet. The gang tried to call out for help, but no one on the ferry heard them and so they were left stranded in the ocean. 
"What will we do now?" May asked, worried.
"Don't worry, I have my Milotic on me so she can give us a ride." Ash said.
Ash was just about to call out his Milotic, but then a red submarine came out from underneath the gang.
"How do you like that?" Brock said. "We don't need Milotic after all."
"I wouldn't celebrate if I were you guys." Ash narrowed his eyes. "This is Team Magma's submarine." 
"Are you sure about that?" May asked him.
"Ash is right." Tomo agreed with his brother. "Officer Jenny showed us a picture of this submarine before."
"I remember. It was sometime after we last encountered Team Aqua and Magma." Max said.
"What do we do?" May asked.
Before anyone could think of a plan, someone was preparing to come out of the sub. The gang quickly hid so they wouldn't be seen. The somebody that came out of the sub was Team Magma's commander Tabitha. The gang saw Tabitha but Tabitha didn't see them. 
"This is Team Magma's sub all right." Brock said. 
"Then they must be up to something." Ash replied.
"What should we do?" May asked.
"It's too late for us to try and escape." Brock said.
The submarine started to move towards a big fortress in the middle of the ocean.
"I bet that's Team Magma's base." Brock said. "And if it is, we're in big trouble."
Brock was right. It was Team Magma's base and they were in trouble. Once the submarine docked the gang was spotted by Team Magma's leader. The boss of Team Magma was a man named Maxie.
"What do you intend to do with us?" Ash demanded. 
He wasn't thrilled to see Team Magma.
"Don't worry kid, I'm just going to keep you here until our mission is complete." Maxie said.
"My apologies sir." Tabitha said. "I didn't realize we had intruders on the submarine sir." 
"It's quite all right." Maxie said. "Bring those kids to my office so we can talk."
Some Team Magma grunts surrounded the gang and led them away. Maxie also asked if there were signs of Team Aqua.
"We have found out that they've made some moves underwater and we believe that they may head over to Monsu Island." Tabitha said. 
"I see, so that means we will be meeting up with Team Aqua soon." Maxie said.
Another intruder was also in Team Magma's base. It was Team Aqua's commander Shelly. The truth is Team Magma had somehow captured Kyogre who Team Aqua was searching for and Team Aqua learned that. So Shelly sneaked on board to release Kyogre.
In Maxie's office, he asked the gang to sit on the sofa so he could talk to them. Max and May were scared of Team Magma, especially their four angry Mightyena. Tomo and Brock were a bit nervous and Ash gave him a blank stare.
"I take it you don't like us very much Ash." Maxie noted.
"Why would I?" Ash questioned back. "You and Team Aqua are fools that plan to use Groudon and Kyogre for selfish purposes." 
The Mightyena growled to silence him.
"Watch your mouth kid!" An unhappy Tabitha demanded.
"Or what?" Ash snapped. His eyes had changed shape in the process. 
Tabitha had no idea who he was threatening. 
"It's all right Tabitha." Maxie said. "We are not exactly the villains that you think we are Ash. You see Team Aqua wants to control all the oceans of the world while we just want to control the land so we can make the world better by expanding the land."
"You have no idea what you're dealing with regarding Groudon and Kyogre. Those two super-ancient Pokemon should not have been reawakened." Ash told Maxie.
Just then a orb appeared on Maxie's desk. It was the Red Orb.
"The Red Orb." Ash said.
"Oh, so you know about this ancient treasure then?" Maxie asked. "With this Red Orb I will be able to control Groudon once I obtain it."
"You won't be able to." Ash argued. "Groudon and Kyogre are way too powerful for anyone to control. If you and Team Aqua think that you can pull that off with the Orbs, you're a lot stupider than I thought."
"Hey!" Tabitha shouted. 
Maxie shushed him.
"I reassure you Ash, I have gone through every little detail about Groudon and this treasure so I will be able to control Groudon once I get it back from Team Aqua." Maxie said.
"What on earth do you mean?" Brock asked.
Maxie explained that his team had captured Kyogre and Team Aqua had captured Groudon. The gang wasn't happy about that, especially Ash.
"So we will be heading to Monsu Island where Team Aqua will be to get Groudon from Team Aqua." Maxie said. "But I'm afraid we can't have you kids mess with our plans, so I'm afraid you will have to be locked up for a while."
Ash was about to attack, but there was an explosion in Team Magma's base. What had happened was Shelly had successfully freed Kyogre from it's cage in Team Magma's base. Then once Kyogre woke up from it's sleep Team Magma placed it under, it created a hole in the base and set itself free. After setting Kyogre free Shelly got ready to leave the base feeling very pleased with her success. Suddenly Shelly was stopped by a man in a Team Magma uniform.
"You're not really a member of Team Magma are you?" The man asked.
"That's right, I'm not." Shelly smiled.
She revealed herself to be a Team Aqua member and then she jumped into the sea. The man was not a Team Magma member either; he was really a disguised Lance. 
Lance had learned about Team Aqua and Team Magma and came to the Hoenn Region to stop them.
Back in Maxie's office...
Maxie was telling his team to evacuate the base. Suddenly the Red Orb was knocked off the desk by an explosion. 
Ash released Pikachu from his Poke Ball after swapping Latios for it.
"Pikachu, grab the Red Orb!" Ash commanded.
Tabitha ordered the Mightyena to attack and grab the orb, but Pikachu beat the Mightyena to it first. Then red markings appeared on Pikachu and then the Red Orb went into Pikachu's body like it bonded with him.
"Grab that Pikachu!" Maxie demanded after seeing what happened.
The Mightyena charged at Pikachu, but it blasted them with Thunderbolt.
"That Thunderbolt was a lot more powerful than a normal Thunderbolt!" Brock gasped.
"And look there are strange markings on Pikachu." May said.
She was right; there were some red markings all over Pikachu causing it pain.
"It's probably related to the Red Orb entering Pikachu's body." Ash said.
There was another explosion and Maxie and Tabitha were knocked off their feet.
"Quick let's get out of here." Brock advised.
Ash grabbed Pikachu while he was knocked out and returned him to the Poke Ball. Then he and the others ran out of the office.
Outside in the middle of the ocean...
Onboard Team Aqua's sub, which was a grayish-blue color Shelly was speaking with her boss. Team Aqua's boss was a man named Archie and he looked like a pirate captain.
"You did a great job releasing Kyogre Shelly." Archie said. 
"Thank you sir." Shelly smiled.
"Now it's time to try out Kyogre's power." Archie said. He had the Blue Orb in his hand.
"Come forth beast of the sea Kyogre." Kyogre emerged from the sea on command; this meant Kyogre was under Archie's control. 
Archie ordered Kyogre to attack Team Magma's base and it fired Hyper Beam at the base.
"Kyogre is more powerful than I thought." He laughed.
No doubt about it Archie was a evil man.
Back at Team Magma's base...
Lance saw something bad was happening and he had to do something about it. Suddenly he noticed Ash and the others, who were about to jump out of the base.
"What are Ash, Brock and Tomo doing here?" Lance asked himself.
May and Max were scared to jump off the base, but Ash told them they didn't have a choice because it was their only way to escape. Suddenly a jolt of the base tossed May, Max, Tomo and Brock into the sea leaving Ash and Pikachu, who was out of his Poke Ball once again, behind. Ash was about to jump off next but Tabitha and two Mightyena stopped before he could jump off.
"Sorry kid, but you and your Pikachu aren't going anywhere." Tabitha smirked.
Max, May, Brock and Tomo saw that Ash had been captured. 
"What should we do?" A worried Tomo asked.
Team Magma led Ash to a cargo room in their flying ship, where he would be imprisoned with Pikachu.
"Where's Maxie?" Tabitha asked a grunt.
"He already headed to Monsu Island." The grunt answered.
"Then that's where we will go." Tabitha said.
As soon as Team Magma took off in their flying ship, Archie ordered Kyogre to attack Team Magma's base again. This time Kyogre's Hyper Beam attack smashed the base some more and it fell into the sea. Archie laughed at this; he was a cruel criminal. The bad thing was that because of the blast the sea acted rough and Brock, Max, May and Tomo were tossed under the water. They were in big trouble, but then a red Gyarados saved them; it was Lance's Gyarados.
On Monsu Island, which was a small island in the middle of the ocean Jessie, James and Meowth were just picking themselves up from their recent blast off from the gang.
"Hey where are we?" Jessie asked.
"I'll look it up in my map book." James said, looking through his book. "Hmm it seems we are at a island called Monsu Island."
"Well that's going to know." Jessie said. "But what should we do now?"
Just then they noticed a flying ship above them.
"Hey that was Team Magma, wasn't it?" Jessie asked.
"It was." James answered. "Which means Team Magma is here."
"Let's go see what they are up to now." Meowth answered.
Team Aqua and Team Magma met up with each other by a pyramid-shaped building that stood on Monsu Island.
"So nice to see you Maxie." Archie said.
Two Aqua grunts revealed two Magma grunts tied up.
"As I recall these two tried to take Groudon but they failed, not a good way of doing business Maxie." 
"Listen here Archie." Maxie replied. "You and I know that Groudon isn't important for your organization. So just hand it over."
Archie laughed.
"Sorry but I won't." He said. "I have obtained Kyogre so I will keep Groudon too."
He showed the Blue Orb to Maxie.
"I propose that you and your team disband and let Team Aqua take over, or I will show no mercy to you with Kyogre." Archie was real power hungry.
Jessie, James and Meowth watched and listened to everything from a hill not far from where Team Aqua and Magma were standing. 
"Goodness me, Team Aqua really is power hungry." James said. "And both Team Aqua and Team Magma really hate each other's guts."
"This makes me glad that Team Rocket is the only criminal organization in Kanto." Jessie said. "I'd hate to have a rival organization to fight against all the time." 
"We should do something; I mean Team Aqua and Magma wish to take over the world. But our boss is the one who should rule the world."
"That's right." Jessie said. "I mean when we told our boss about Team Aqua and Team Magma when we first met them, he said we should deal with them. But Team Aqua has both Kyogre and Groudon and those two Pokemon are legendary Pokemon."
"Then how about we release them from Team Aqua." James advised. "Remember how we released Moltres and Zapdos from that weird Pokemon collector in the Orange Islands."
"Oh yeah; his plan to capture all three legendary birds failed after we released Zapdos and Moltres." Meowth said.
"That's right." James said. "So if we release them, then Team Aqua's scheme to rule the world will fail."
"I like that idea, so let's do it." Jessie added. 
"Yeah, let's ruin Aqua and Magma." Meowth agreed. "And make Team Rocket number one again."
Back in Team Magma's ship, in the cargo hold...
Pikachu was still in pain and giving off electricity due to fusing with the Red Orb. Ash instructed his Marshtomp to hold Pikachu; since it was a water/ground type he could withstand Pikachu's electricity. 
"Hang on tight Marshtomp and don't let go." Ash said.
Marshtomp nodded. Ash then removed his Master Ball from his backpack; it was time to ask for Mewtwo's assistance.
'Mewtwo, I need your help.' He said.
'Ash, I'm glad you contacted me.' Mewtwo said. He was flying across the ocean. 'I sense a real disturbance in the ocean, what happened?'
"It's Team Aqua and Magma." Ash said. "They're making their move, they've captured Kyogre and Groudon and they've got the Red and Blue Orbs." 
Mewtwo was not happy about that. 
'Where are they?' He asked.
"Monsu Island. I'm there too." Ash said. "Hurry up, I'm afraid that something really bad is going to happen."
'I'm on my way to Monsu Island now, so I'll be there soon.' Mewtwo replied.
"Okay and I'll be ready to summon Rayquaza when it's necessary." Ash said. 
They finished speaking.
Then Lance, in his Team Magma disguise entered the room.
"Ash, it's me Lance." He said, revealing his face.
"Good to see you here." Ash replied. 
He told Lance about what he knew about Team Aqua and Team Magma wanting to control Kyogre and Groudon with the Red and Blue Orbs.
"I already know, that's why I'm here." Lance responded.
"The Red Orb inserted itself into Pikachu's body and I'm worried for his safety." Ash said. 
"The Red and Blue Orbs are dangerous artifacts and if someone is in contact with them for too long their minds will be corrupted." Lance explained. "Which is why both Pokemon and humans have to be careful when around them. But don't worry Ash, I will find a way to help Pikachu out."
"Lance, there's something you should see and know about." Ash replied. He took the Jade Orb out of his backpack and told Lance it was to summon Rayquaza. 
"Ash, how did you get that?" Lance asked in surprise.
Ash explained to Lance that he had a legendary Pokemon called Mewtwo.
"My friends and I found out some time ago that Team Magma wished to control Groudon and we figured that Team Aqua would be after Kyogre, and that gave me the idea that we would need Rayquaza's help. So Mewtwo found Rayquaza who lives in outer space and asked it to help us. That's where I got the Jade Orb from; Rayquaza agreed to help us and gave the Jade Orb to us." Lance was fascinated by this.
"I actually feel relieved that Rayquaza is going to help us because we're going to need all the help we can get." He said. "Ash I need you to be patient and wait here a bit more until I figure out what to do from here." 
Ash agreed to stay patient. 
Outside on the ocean Brock, Tomo, May and Max were still riding on Lance's Gyarados. Brock and Tomo explained to Max and May about their encounter with Lance in the Johto Region and about him being a member of an organization called the G-Men.
"You guys are lucky to have met Lance, a member of Kanto's Elite Four." Max said.
"I'm relieved that we have an ally on our side here to help us." May said.
"I hope Ash and Pikachu are all right." Tomo said. He was worried about his brother.
"I hope so too." Brock replied. "Which is why we need to get to Monsu Island quick."
"Full speed ahead please Gyarados." Tomo said to Lance's Gyarados.
Meanwhile...
Jessie, James and Meowth spotted Team Aqua's sub.
"Let's get this party started." Meowth said.
"Wait a minute, I see some Aqua grunts guarding it." James noted. "We need to get in there without being discovered."
"Not a problem." Jessie smiled.
She handed a male Team Aqua uniform to James and presented a female Team Aqua uniform. 
"Wow, Jessie where did you get these from?" James asked.
"Let's just say that I borrowed a pair of these uniforms the last time we saw Team Aqua." Jessie said.
The truth is, she actually stole the uniforms. She and James changed into the uniforms.
"You know I like this uniform." James said. "I think I'll take a Magma outfit too."
"Me too." Jessie agreed.
"Hey, how come I don't have a uniform?" Meowth asked. 
"Because Meowth, you are a Pokemon and you take the role of being our Pokemon." Jessie reminded him.
Meowth conceded the point.
Jessie, James and Meowth calmly walked towards the Aqua sub in their disguises. Meowth stayed quiet so he didn't ruin the disguise. Just then they were stopped by two Aqua grunts. 
"What are you two doing here?" A female grunt asked.
"We saw somebody walking towards one of the cargo holds." James lied, winking at Jessie. 
"We think someone is trying to get to Kyogre or Groudon." Jessie said.
"Let's check the cargo hold with Kyogre." The female grunt suggested.
"Let's." The male grunt agreed.
They typed in something on a computer and opened one of the cargo holds. This hold contained Kyogre.
"Hmm everything looks normal in here." The male grunt said.
Suddenly they ended up drifting off to sleep. This was James' doing; he ordered his Roselia to use Grass Whistle and it put the grunts to sleep.
"Great work there." Meowth said. "Now let's release Kyogre."
The trio found Kyogre sleeping in an enormous tank of water.
"Kyogre looks exhausted don't you think?" Jessie questioned.
"Team Aqua must have knocked it unconscious." Meowth said.
"Leave this to me." James smiled.
James released his Chimecho and told it to use Heal Pulse. Heal Pulse was a move that allowed the user to heal another Pokemon. Kyogre started to recover and then it woke up. It saw the trio.
"We are getting you out of here Kyogre." Meowth said.
He started to use Swift to break Kyogre's tank; this way it would help Kyogre break out. Just then Kyogre used Hyper Beam to break it's container and then it jumped into the sea. 
"Mission completed." James smiled.
"Come on, let's get out of here before Team Aqua finds out." Meowth said.
The trio quickly left the sub.
At that moment storm clouds formed in the sky and Archie received word his sub was attacked.
"I don't suppose you had anything to do with this Maxie?" Archie asked.
"How can I since my team and I just evacuated our sunken base." Maxie replied.
Tomo, Brock, May and Max had just arrived on Monsu Island and noticed the dark clouds in the sky.
"I don't like the looks of this." Tomo said, looking up at the sky.
"Me either." Brock said. "We better find Ash and Pikachu. I have a bad feeling that something bad is going to happen."
Things got worse after Kyogre escaped Team Aqua's sub; a big and terrible storm was brewing. This was because of Kyogre's ability Drizzle, which generated rain. Mewtwo was flying near the area.
'I must find Ash quickly.' He said to himself.
He could sense that something terrible was happening.
Right now Archie with the Blue Orb was now ready to fully control Kyogre.
"Maxie prepare to see Team Aqua take over the whole world." Archie said.
Shelly and the Aqua grunts called out to their Walrein to attack Team Magma. Tabitha and the Magma grunts called out their Mightyena to fight back. Archie saw the opportunity to get onto a miniature aircraft, a machine that can fly, to experience everything from the air. By now the storm was really bad and getting very, very rough and dangerous. 
"Hey Maxie." Archie said. "I was going to let you watch me become the ruler of the world, but it seems you won't be able to witness my triumph. It won't be long before Kyogre and I flood all of Monsu Island and you with it."
"Are you crazy?!" Maxie shouted. "Your own team is here too."
"So what?" Archie scoffed. 
Archie was willing to sacrifice his own team for his triumph. The truth is he had become very power hungry and berserk because of his control of the Blue Orb. 
Shelly couldn't believe that Archie was betraying his own team and the Aqua grunts were angry with Archie. Lance could tell that Archie had become a real control freak. Tabitha told the Magma grunts to gather up the Pokemon and take shelter in the building and Shelly told the Aqua grunts to do the same thing.
Lance removed his hood and explained to Maxie that the Red and Blue Orbs were created by evil people who planned to use Groudon and Kyogre as weapons in ancient times. But the powers of Groudon and Kyogre were more than the ancient people thought of. The more evil the two Pokemon became, the more things got out of hand and the people controlling them became more evil and corrupted.
"That's why the Orbs were sealed away; it was to prevent people from making the same mistake again."
"But this can't be." Maxie said. "We analyzed the Orbs and came to the conclusion that only weak people could become corrupted by the Orbs. And we need the Pokemon to build a better world." 
"How can you believe that nonsense?!" Lance shouted. "It's because of you and Archie that the Hoenn Region is now in danger!"
Maxie flinched.
By now Mewtwo had arrived at Monsu Island and he saw the situation. Then he found Ash and Pikachu in Team Magma's base.
'Ash, I'm going to get you out of there now.' He said.
"I can get myself out." Ash replied before leaping out of the base.
Then Pikachu started acting up again and ran off.
'What's wrong with Pikachu?' Mewtwo asked.
Ash explained that the Red Orb bonded with Pikachu and caused him to go crazy.
"What's going on with Team Magma and Aqua?" Ash asked.
'It's not good.' Mewtwo said. 'The boss of Team Aqua has gone mad and Kyogre is starting to cause destruction.'
"In that case." Ash sighed after returning Marshtomp to his Poke Ball. "Form Change Dragon. If push comes to shove, I'm going to stop Groudon and Kyogre."
Just then Tomo, Brock, May, Max and Lance showed up. Tomo, Brock, May and Max were relieved to see that Ash was all right. Mewtwo took off his mask and the top of his cloak to reveal himself to Lance. Lance, May and Max were surprised to see Ash's Mewtwo in person.
"Pikachu ran off and the symbols on his body appeared again." Ash told them. "And it's giving me the feeling that Groudon is somewhere behind it."
'I sensed Groudon's presence when I saw Team Aqua's sub.' Mewtwo said. 'So Pikachu might be heading there.'
"Then that's where we're going." Ash said. "Brock, you, Tomo, May and Max follow Pikachu. I'll keep Groudon and Kyogre from fighting."
"And I'll try to stop Archie." Lance said.
He called out his Dragonite and they took off into the sky.
Meanwhile...
Jessie, James and Meowth were trying to take shelter from the fierce storm.
"I don't know about you guys, but this predicament is worse than the one we had in the Orange Islands when the three Legendary Birds fought each other." Meowth said.
"Yeah I remember that." Jessie said. "So we better head to shelter."
"I thought you would say that so I did make a shelter for us to hide in." James said.
He presented a sort of ball-shaped bush made out of vines, mud, sticks and leaves.
"With the help of my Pokemon we were able to make this shelter." 
"Excellent James, now we'll be safe until this storm's over." Jessie said.
The trio got into it and agreed not to leave until it was all over.
Right now Lance was trying to stop Archie while on Dragonite.
"Archie, you have to stop this!" He shouted. "If you don't, you might end up being destroyed by the Blue Orb!"
Archie laughed; he wouldn't listen and all he cared about now was using the power of Kyogre.
"Blow that nuisance away with Hydro Pump Kyogre." Archie said.
Dragonite managed to dodge before Hydro Pump could hit it. Lance ordered his Gyarados to use Hyper Beam but Archie told Kyogre to do the same and Kyogre's Hyper Beam was no match for Gyarados's.
Then the Blue Orb in Archie's hand glowed blue and then it went into Archie's body. Archie now had blue symbols on his body and he became more of a maniac.
Meanwhile...
Pikachu had jumped onto Team Aqua's sub and was releasing electricity on it. Brock, May, Max and Tomo arrived and saw what Pikachu was doing.
'I sense Groudon is in there, so Pikachu must be trying to free it.' Mewtwo said.
"Why would Pikachu do that?" May asked.
It dawned on Brock.
"The Red Orb. Pikachu has now bonded with Groudon just like the boss of Team Aqua bonded with Kyogre. So Groudon must have been calling out to Pikachu for help and now he's doing just that."
Pikachu now used Thunder on the cargo hold of Groudon and then it broke apart freeing Groudon.
As soon as Groudon was free, the volcano on Monsu Island started to erupt and lava began to pour of it and into the ocean. Then it stopped raining and the clouds cleared. This was because of Groudon's ability Drought which made the weather sunny, like Sunny Day but stronger. Pikachu jumped on top of Groudon's head, ready to fight with it. As soon as Kyogre and Groudon saw each other, a big tidal wave headed towards Monsu Island. 
"That wave is big enough to cover this whole island." Brock said. 
Then Groudon fired a Solar Beam at the tidal wave and it evaporated.
"That was incredible!" Max gasped.
The gang was amazed by how strong Groudon was.
Maxie and Tabitha, who had followed the gang saw everything.
The leader of Team Magma recalled the warning that was issued earlier in his office.
"You have no idea what you're dealing with regarding Groudon and Kyogre. Those two super-ancient Pokemon should not have been reawakened." 
"We were fools." Maxie admitted. "He was right. Waking Groudon and Kyogre up was a mistake. One we're never going to repeat again." 
He realized his mistake. Shelly, who also followed them, realized as well that controlling Kyogre was impossible. She was worried about Archie's safety.
Before changing forms, Ash had taken his backpack off his back and then took out the Jade Orb. 
"It's time for Rayquaza to make a appearance." He said. 
"Wait Ash, don't do it." May pleaded.
"Yeah otherwise the Jade Orb might possess you like it possessed Pikachu and Archie." Max added.
"What choice do we have?" Ash shot back. "It's the only thing that can calm Kyogre and Groudon down."
"I agree." Lance said after joining the others. "In ancient times, when Kyogre and Groudon attacked each other, Rayquaza served as the peacemaker of the Weather Trio and the Jade Orb was created by good people so that if this ever happened again Rayquaza would help. Please call Rayquaza."
A clawed hand raised the Jade Orb up to the sky. 
"Rayquaza, respond to my call for assistance." He said. "Groudon and Kyogre have been reawakened and are fighting each other. Please free Kyogre from Team Aqua's control."
The Jade Orb then glowed green with green symbols on it and Rayquaza descended from the sky. Rayquaza was under Ash's control since he possessed the Jade Orb. Groudon and Kyogre looked up to the sky and saw Rayquaza. Maxie, Tabitha and Shelly saw Rayquaza too.
"I can't believe it!" Maxie gasped. "What is the legendary Pokemon Rayquaza doing here?"
Archie also saw Rayquaza; he called it another rival to dispose of.
"It's good that both Groudon and Rayquaza are on our side, but they may need some help." Lance said.
"And they're going to get it." Ash flew up into the air.
"Dragonite and I will also see what we can do." Lance added.
"We will help on your Gyarados too." Tomo said.
"Yeah we are not going to leave Pikachu either." Max declared.
Lance agreed to let the gang help.
"What do you want me to do Ash?" Mewtwo asked.
"Find all the Team Magma and Team Aqua members on this island and tie them up." Ash said. "They're the reason this is happening in the first place. It's time to end this once and for all." 
Mewtwo nodded before putting his mask back on and went off to find Team Aqua and Team Magma. 
Ash flew alongside Lance's Dragonite and he and Lance watched what was happening from the air. Despite being a ground type, Groudon could walk through the water without a issue. Right now Groudon and Kyogre were tackling each other in the ocean.
"I don't like this." Ash muttered.
"Neither do I." Lance said. "The one controlling Kyogre is Archie." 
"Where is he anyway?" Ash asked.
Lance pointed to where Archie was. He was watching everything from his miniature aircraft.
"Alright then, let's take the fight to him." Ash held up the Jade Orb. "Rayquaza, distract Archie with Hyper Beam and break his control over Kyogre."
Rayquaza fired Hyper Beam towards Archie, just missing him and the aircraft. Archie didn't like that. 
"Oh so Rayquaza wants to fight too huh?" He questioned. "Okay then, Kyogre attack Rayquaza with Hydro Pump."
Kyogre turned to where Rayquaza was and got ready to attack it. But because Kyogre was concentrating on Rayquaza, it became a easy target for Groudon to attack and Archie realized that a little too late. Groudon fired Solar Beam which hit Kyogre. Because Kyogre was hit by the attack, the Blue Orb left Archie's body, so he no longer had control of Kyogre. Archie lost consciousness and fell off his aircraft but Lance had his Dragonite grab Archie. Because Kyogre was now free the Red Orb left Pikachu's body, so it was no longer bonded to Groudon. Pikachu also lost consciousness and fell towards the sea, but he was caught before entering the water. Ash then noticed Kyogre heading his way and feared he was going to attack them.
On Monsu Island Lance took a still unconscious Archie to shore. Shelly, fearing for her boss's well being, held Archie in her arms and asked him to wake up. When Archie woke up he had no memories of being possessed by the Blue Orb. Then Mewtwo, who was standing next to Lance, grabbed Maxie, Tabitha, Archie and Shelly with Psychic.
'Team Aqua and Magma, your reign of terror ends here.' He said angrily.
Lance immediately called Officer Jenny and told her that Team Aqua and Magma were on Monsu Island. 
Meanwhile...
Ash had placed Pikachu on Kyogre's back after it emerged from the ocean. This meant that Kyogre was helping him and not attacking him; since Kyogre was no longer under Archie's control it was no longer evil. Kyogre, Groudon and Rayquaza stared at each other and growled softly; this meant that the Weather Trio was at peace with each other. Just then Pikachu regained consciousness and Ash was happy to see Pikachu was okay again. Then Lance and Dragonite descended and Ash placed Pikachu on Dragonite's back. Lance was happy that the Weather Trio was no longer fighting. 
"Now Groudon, Kyogre and Rayquaza can live in peace again." He said.
Suddenly the Jade Orb Ash was holding started to glow green. The orb then left his possession and floated into the air. The Red and Blue Orbs did the same thing and then the orbs started twirling around together as if they were dancing before they combined with each other and evaporated. The Red, Blue and Jade Orbs were gone. Because the orbs disappeared, the Weather Trio could return to their domains. Groudon went back to his home, which was actually Monsu Island's volcano, Kyogre dived down to the deep trenches of the ocean and Rayquaza ascended towards the sky. Ash thanked Rayquaza for it's help.
Then the police surrounded Monsu Island and they arrested all the Team Aqua and Team Magma members before placing them in prison boats. A dozen Officer Jenny's who came from different parts of the Hoenn Region were also there and they were speaking to Maxie and Archie.
"Team Magma and Aqua, you have caused a lot of trouble here in the Hoenn Region." Rustboro City's Officer Jenny said.
"Your desire to control Kyogre and Groudon could have destroyed the region." Slateport City's Officer Jenny said.
"So now you will answer for your crimes in jail." Verdanturf Town's Officer Jenny said.
"We will go quietly." Maxie stated". "We realize that it was impossible to control Groudon and Kyogre."
"I agree." Everyone looked up to see Ash floating in the air. "I did warn you about that back on the submarine. Glad to know you're thinking clearly." 
Maxie and Archie knew everything he said was true. They were then placed onto the prison ship. The Officer Jenny's thanked Lance and the gang.
"Thanks to all of you, the Hoenn Region is now safe from Team Aqua and Magma." Lavaridge Town's Officer Jenny said.
"Just make sure they aren't released." Ash replied. "They shouldn't be allowed to roam free."
"Don't worry Ash, they'll be in jail for a long, long time." Littleroot Town's Officer Jenny said. 
Then the police left with Team Aqua and Magma on the ship. It was now the end of Team Aqua and Magma.
So Monsu Island was safe again; because the lava from the volcano had cooled off and hardened, the island had more land.
"I can't thank you kids enough for helping me stop Team Aqua and Magma." Lance said. "Especially you Ash. If it wasn't for you and Mewtwo obtaining the Jade Orb we probably never would have defeated Team Aqua and Magma." 
"I'm glad Rayquaza trusted me with the Jade Orb." Ash said.
"That was no accident Ash." Lance told him. "Rayquaza probably noticed that you really cared about the Pokemon world and so it responded to your feelings."
Ash turned to Mewtwo and asked him what he was going to do next.
'Ash I want you to return me to the Master Ball.' Mewtwo said. 'I have done a lot on my travels so I wish to rest and heal for a while.' 
"I understand." Ash nodded, taking the Master Ball out of his backpack. "I will also send you to Prof. Oak. He knows of your existence so he will make sure you get a good rest and heal up."
So Ash returned Mewtwo to the Master Ball and sent to Prof. Oak's lab. Lance offered to give the gang a lift to Mossdeep City and the gang accepted it because it was their next destination. So now that the issue with Team Aqua and Magma was finally over, the gang could now enjoy their journey with no more disturbances from Team Aqua and Magma.
Elsewhere...
Jessie, James and Meowth were flying with their rocket backpacks. They saw the arrest of Team Aqua and Magma and they were pleased.
"Team Aqua and Magma have been defeated." Jessie laughed.
"The boss will be happy to hear about this." Meowth said.
"Let's hope that there are no other organizations apart from Team Rocket elsewhere." James said. 
"If there are we'll just bring them down." Meowth said.
So the trio left Monsu Island as well, happy that Team Aqua and Magma were taken care of.