Creation Trio

Ash, Brock and Dawn wanted to grab the Lake Guardians to save them, but Purugly and Skuntank stopped them with Iron Tail.
Their Toxicroak used Sludge Bomb to push Pikachu, Piplup and Croagunk back. Brock immediately returned Croagunk to it's Poke Ball.
Cyrus stepped forward and the Lake Guardians flew behind them.
"Azelf." Ash said.
He got a good look at the guardians. 
"They are being controlled."
"What?" Dawn gasped.
"We have the Red Chain which possesses the power of the Original One so as you can see they are now under my control." Cyrus said.
He revealed the red shard gem on his glove to the gang. 
"You see, according to legend these powers are responsible for reshaping our entire world so no Pokemon will be able to withstand them." Charon said. 
"It is with these powers that I will be able to create a new world." Cyrus said.
"You can't do that!" Dawn shouted, glaring.
Cyrus ignored her words.
"Take care of them." He ordered Saturn before walking off with the lake guardians.
Ash, Dawn and Brock were captured by the grunts and there was nothing they could do to stop Team Galactic right now.
Before long Team Galactic was flying in a helicopter on the way to Spear Pillar. Ash, Dawn and Brock were taken prisoner and they were handcuffed while Piplup was chained up.
"What's going to happen to us now?" Dawn asked, worried.
"Cyrus is using us as hostages so that Uxie and the others will do as he says." Brock said. "We're part of his backup plan in case they do break free from his control." 
"Let's hope that Cynthia and Tomo will be able to find us." Ash said. "And once they do we'll use the Griseous Orb to call Giratina for help."
Dawn and Brock agreed.
Meanwhile...
Cynthia and Tomo were driving through Mt. Coronet.
"Hey Cynthia, look up there." Tomo said, pointing to the sky. 
It was Team Galactic's helicopter. Cynthia made the jeep go faster so they could follow the helicopter to wherever it was going. Tomo held onto Ash's backpack tight so he wouldn't lose it.
At the entrance of the Spear Pillar the Team Galactic grunts were all tied up. This was because Jessie had used her Yanmega to take them out; she had brought her Pokemon with her just in case and James had his Pokemon with him too. So now she, James and Looker were guarding the entrance disguised as Team Galactic grunts. Just then the helicopter arrived.
"They're here." Looker said. "And most likely with Team Galactic's leader on board."
"Good, it's about time we met the leader." James said.
"Now we can get even with all of Team Galactic." Jessie said.
"I'm more than ready to fight." Meowth said.
The helicopter soon landed and Cyrus came out of the helicopter with Saturn, Jupiter, Mars and the lake guardians. Looker and the trio were surprised when they saw Cyrus.
"Hey, that's the man we met at the Celestic Ruins." James whispered.
"Yes, the one who gave us an annoying speech." Jessie whispered.
"So that's the boss." Meowth whispered.
Jupiter suddenly released her Skuntank.
"Flamethrower." She ordered.
The stream of fire burned Looker, Jessie and James' disguises; they saw right through them and weren't going to fall for their tricks. Looker and the trio were immediately captured and placed in the prison cell the gang was in.
"They caught you as well?" Looker asked, surprised to see the gang again.
"Why are you here?" Brock asked. "And why are you with Jessie, James and Meowth."
Before any questions could be answered Jupiter shut the door with a smirk.
"Let us out of here right now!" Ash demanded.
Jupiter ignored him.
"Keep a eye on them for now." He told a grunt.
"Grr foiled by Team Galactic again." Looker growled.
"So why are you here Team Rocket?" Dawn asked.
"James, Meowth and I are no longer part of Team Rocket, thank you very much." James said. "And to answer your question we have a score to settle with Team Galactic." 
Dawn just stared at them.
Outside
Cyrus and his team stood in front of the entrance to the Spear Pillar.
"The spear key." Cyrus said to Saturn.
Saturn placed the key in front of the entrance. The key glowed and so did the entrance, then the key flew into a golden orb on the entrance and the entrance revealed a stone wall door. Cyrus touched the orb and the door opened, revealing a passage way down into the mountain. Then the bright orb flew down the passage way and revealed some stairs. 
"This means that the Spear Pillar must be somewhere deep within that passageway." Charon said.
"Exactly as it was written in ancient times." Cyrus said.
He and the team started to go down the stairs taking the Adamant and Lustrous Orbs and the Lake Guardians with them, except Jupiter. She was ordered to stay behind and guard the entrance.
"Oh, why do I have to stay and guard this thing anyway?" Jupiter groaned.
She really wanted to join the others and watch the action.
Suddenly Cynthia's Garchomp charged in with Giga Impact and Skuntank was knocked out.
Cynthia and Tomo appeared out of nowhere. Jupiter was about to release another Pokemon but Garchomp stopped her by holding it's claws to her neck.
"Now where are they?!" Cynthia demanded.
Jupiter had no other option but to disclose their whereabouts.
They headed to the prison cell and opened the door. Ash, Brock, Dawn and Looker were happy to see Cynthia. Cynthia and Tomo removed Brock, Dawn and Looker's bindings.
Ash didn't need them to remove his bindings as he freed himself using all his strength.
Tomo then handed him his backpack.
It wasn't long before Jupiter and her men were tied up and placed in the prison cell.
"Hah, I've wanted to get back at you for ages." Jessie teased.
"Even though you've caught me, it's too late." Jupiter smirked. "The world you know is coming to a end."
"That's not going to happen!" Ash shouted. "This isn't the first evil organization I've taken down and I'll do again. Come on guys. It's time for us to bring Team Galactic down for good."
Dawn, Brock and Tomo agreed as did Cynthia.
They ran out of the plane to get to Spear Pillar, leaving Looker and the trio behind to watch over Jupiter and the rest of the Galactic grunts.
Inside the depths of Spear Pillar were some ancient ruins. On the floor was a big triangle shaped stone slab with five stone pillars on it. Azelf, Uxie and Mesprit flew over to three pillars that surrounded the stone slab and Saturn and Mars placed the Adamant and Lustrous Orbs on the pillars in the center of the slab. 
"Azelf, Uxie and Mesprit hear me now." Cyrus said. "Transfer your powers to the Adamant and Lustrous Orbs and use it to connect to time and space."
The lake guardians did as they were told and transferred their power to the orbs. 
"Fire." Charon ordered the grunts to fire the cannon they brought with them.
What shot out of the cannon were two big red chains that Charon had created before.
The red chains formed two big circles and then the Adamant and Lustrous Orbs opened up portals leading to Dialga and Palkia's dimensions. Charon was impressed with the amount of energy produced by this.
"Dialga and Palkia the time has come." Cyrus said. "Reveal yourselves now."
Shadows of Dialga and Palkia and the red chain surrounded their bodies immediately, trapping them. Saturn and Mars were amazed by this.
Suddenly a Thunderbolt attack destroyed the cannon. Pikachu was riding on Staraptor, Piplup was riding on Ash's Gliscor, and Growlithe and Croagunk were riding on Garchomp. Saturn released Toxicroak to fight back, but Croagunk jumped off Garchomp and whacked Toxicroak really hard on the head with Brick Break. Toxicroak was quickly knocked out and Croagunk got payback. Cynthia and the gang then ran forward and saw the shadows of Dialga and Palkia.
"Dialga, Palkia and the three lake guardians." Cynthia said. "I've always wanted to meet them, but not like this."
Ash quickly opened his backpack and took the Griseous Orb out. It was time to get Giratina's help. Cynthia was amazed by the Griseous Orb's beauty.
"Huh, what is that?" Charon asked, looking at the orb.
He had no idea about the Griseous Orb's existence.
Ash proceeded to raise the Griseous Orb in the air, ignoring Charon's question.
"Giratina!" He shouted. "Come forth and help us free Dialga, Palkia and the lake guardians from Team Galactic!"
Just then a portal opened and Giratina emerged from it.
"I don't believe it!" Charon said. "It's Giratina, the Pokemon of antimatter."
"Why didn't you tell us there was a orb for the legendary Pokemon Giratina, Charon?!" Saturn shouted.
"Because I had no idea." Charon said. "There's no information regarding it. How did that kid know about that orb and how did he get it?"
There was no time for Charon to look for answers. Giratina saw what was happening and became angry with Team Galactic. Mars and the grunts sent out Purugly and Golbat to fight, but it was no use. They were easily blown away by Giratina's Dragon Breath. This gave the gang a chance to save the lake guardians.
"Pikachu, Thunderbolt."
"Piplup, Bubble Beam." Dawn ordered.
"Croagunk, Brick Break." Brock ordered.
The attacks broke the shards on the Pokemon's head and the legendary Pokemon were no longer being controlled. Ash, Dawn and Brock quickly ran over to them.
"Azelf, I'm here." Ash said, holding it in his arms.
"Mesprit, it's me." Dawn said, holding it in her arms.
"Uxie, it's Brock." Brock said, holding it in his arms.
The lake guardians were happy to see their chosen three.
Because the lake guardians were not spreading energy on the stone mosaic, Dialga and Palkia's shadows started to disappear. 
"You no longer have the power to control Dialga and Palkia." Cynthia told Cyrus.
She was wrong though as Cyrus still had a piece of the Red Chain shard on his glove. This was his backup plan. He gave more energy to the formations and Dialga and Palkia were fully visible. 
"Oh no, they're here." Dawn said.
Dialga and Palkia began to roar in pain because they were being placed under the control of the Red Chain. The Red Chain had the ability to control them like it controlled the lake guardians. Giratina was really angry now and fired a Aura Sphere, but Team Galactic's Golbat took the hit so Giratina wouldn't get in the way. Just then the lake guardians flew out of Ash, Brock and Dawn's arms and started communicating with them telepathically.
"I hear you." Ash said. "You want us to help save Dialga and Palkia."
Dawn and Brock also understood what they were saying.
"Use your powers and create a new universe." Cyrus ordered Dialga and Palkia.
The power created a portal to another dimension. This was bad because the Pokemon would be destroyed if this new world was created. Outside a dangerous thunderstorm was brewing because of the amounts of energy being produced by the legendary Pokemon. Jupiter knew what was happening.
"A new world is about to be born." She revealed.
"Is this what you want?!" Looker shouted. "You'll die with the rest of us!"
"That's okay with me." Jupiter smiled.
She didn't care what happened to her as long as Team Galactic successfully created a new world.
Back inside Mt. Coronet
Things were looking bad.
"I am the one who is finally going to bring order to this chaos." Cyrus said.
"We're not gonna let that happen!" Ash shouted.
Suddenly Giratina released Shadow Force towards Dialga and Palkia.
"Use Spacial Rend." Cyrus ordered.
"You have to destroy the red chains." Cynthia told the gang. "If you destroy the chains Dialga and Palkia will no longer be controlled and we can stop the creation of the new world."
The gang nodded.
"Take out the rings." They ordered their Pokemon to attack.
Pikachu used Thunderbolt, Growlithe used Flamethrower, Piplup used Bubble Beam and Croagunk used Poison Sting.
"Counter with Roar of Time." Cyrus ordered.
Roar of Time overpowered their attacks and made it's way towards the gang. At the last second, the lake guardians used Protect.
"You saved us. Thank you." Dawn said.
Saturn and Mars were happy the new world was about to appear.
"Take us with you." They asked Cyrus.
Cyrus had no intention of doing that.
"I have no need for you now." He said. "Your very existence will poison my new world."
These words meant Cyrus had been using the rest of Team Galactic as pawns the whole time; he had no intention of ruling the world with anyone else. Team Galactic was in disbelief that this whole time they were merely pawns. Charon seemed to be aware of it though. While Cyrus was distracted Giratina attacked with Shadow Force and this time the attack struck Dialga's ring. Azelf, Uxie and Mesprit understood what Giratina was doing and used Extrasensory on Palkia's ring. The Red Chains were destroyed and Dialga and Palkia were freed. The portal then began to close.
It wasn't over yet. Dialga and Palkia went on a rampage because of what Team Galactic did to them. They used Roar of Time and Spacial Rend to create a massive black hole. This was really bad because the black hole could destroy the Sinnoh Region. Giratina tried to stop their rampage by roaring at them, but it was no use. All Team Galactic could do was take cover. Cynthia approached the gang.
"I'm sure Dialga and Palkia haven't broken free. We need to save them otherwise Sinnon is doomed." She said.
Just then the lake guardians spoke to Ash, Dawn and Brock.
"They need our help." Ash said.
"Combine our hearts as one." Dawn said.
"And please save Dialga and Palkia." Brock said.
"Come on, let's help them." Ash said.
Ash, Brock and Dawn stood in front of the black hole with the lake guardians.
"Alright Azelf, let's do it." Ash said, merging with it.
Azelf flew towards the black hole and used Explosion to stop it. It was exhausted fell into Ash's arms. 
"Thank you Azelf. You did it." Ash said.
Next Brock and Uxie merged to end Dialga and Palkia's rampage.
"Dialga, Palkia your tormentor is gone. Please calm down." Brock begged.
Uxie's power ended their rampage. Speaking of Uxie, it then fell into Brock's arms.
"Thank you so much Uxie." Brock said.
Now it was time for Dawn and Mesprit to merge. Mesprit's power fully healed Dialga and Palkia so they were officially no longer under Team Galactic's control.
"Thank you Mesprit." Dawn said.
Just then Giratina growled.
"Is Giratina angry with Dialga and Palkia?" Dawn asked, worried.
"No." Ash answered. "It's happy that Dialga and Palkia are back to normal."
He was right because Dialga and Palkia thanked Giratina for it's help. They were no longer at odds. Just then the lake guardians created a portal that helped Dialga and Palkia return to their respective dimensions. The crisis had finally come to a end.
After Dialga and Palkia returned to their home dimensions, Giratina let out a soft growl. It was going to return to it's dimension. Ash walked over to Giratina with the Griseous Orb in his hands. 
"Thank you Giratina." Ash said. "We couldn't have freed the legendary Pokemon without your help."
Giratina growled happily and then used Psychic to lift the orb out of his hands. Then Giratina returned to it's dimension with the orb.
"What happened?" Dawn asked.
"Giratina uses that orb to protect it's dimension." Ash said. "So it really needed the Griseous Orb back."
"I see." Dawn said. "Well I'm glad Giratina helped us."
"That was no accident." Cynthia said. "Even though Giratina is said to be a very violent Pokemon; it sensed your desire to stop Team Galactic and help the legendary Pokemon."
Dawn smiled. She fully understood it now.
Meanwhile
Prof. Rowan and his assistants along with Gary had noticed on the computers how calm everything was on Mt. Coronet. They had been examining everything and observed the energy disturbances on Mt. Coronet with their computers. Prof. Rowan was worried about Ash, Dawn, Brock and Tomo.
"We need to get to Mt. Coronet right away." He declared.
Back inside the Spear Pillar
The lake guardians surrounded Ash, Dawn and Brock thanking them for everything.
"So Azelf, Uxie, Mesprit." Ash said. "Why did you choose us?"
"I have the answer." Cynthia said. "They can sense how much you care about Pokemon."
"Is that so?" Ash smiled.
Just then Azelf, Uxie and Mesprit made three Dive Balls appear in front of them.
"Hey these are Dive Balls." Brock said, grabbing one.
Ash and Dawn grabbed the other two.
The lake guardians spoke to the three.
"What? You want us to capture you?" Ash asked.
The three Pokemon nodded yes.
"But what about your lakes?" Dawn asked. "You need to resume guarding them."
The three Pokemon spoke again.
"Oh you're saying a Azelf, Uxie and Mesprit have just been born." Ash said. "They're going to be the new lake guardians while you spend the rest of your lives with us."
The three Pokemon nodded yes.
"Well, well, well." Cynthia said. "This is unexpected. Ash, Dawn, Brock, will you agree to the lake guardians request?"
They looked at each other and smiled.
"We welcome you to our teams." Ash told the three Pokemon.
The lake guardians tapped the Dive Balls and were caught immediately.
"I can't believe we really caught Azelf, Uxie and Mesprit." Dawn said.
"Wait till Prof. Oak finds out about this." Ash said.
"We'll take good care of them." Brock said. 
Tomo thought they were lucky and wished he could capture his own legendary Pokemon.
Meanwhile
Looker was talking to Jessie, James and Meowth.
He was thanking them for their help.
"Think nothing of it sir." Jessie said. "I'm glad we were finally able to get even with Team Galactic."
"Now that that's over I need to get back to Christopher." Meowth said. "I promised Glameow I wouldn't be gone for that long."
"Yeah I need to get back to my job in Hoenn too." James said.
"Same here." Jessie added.
"Alright." Looker said. "Thanks again for helping me."
"See ya." Jessie, James and Meowth said goodbye to Looker.
They then left Mt. Coronet in their balloon.
It wasn't long before the police arrived with Prof. Rowan, Caroline and Gary. Prof. Rowan and Gary were glad to see they were alright. The Team Galactic members were quickly arrested and Cynthia and the gang informed them about what had happened. The gang even told them about the captures od Azelf, Uxie and Mesprit.
"So you've caught another legendary Pokemon, huh Ash?" Gary asked.
"I'm afraid so." Ash said.
"You better take good care of the three lake guardians Ash, Dawn, Brock." Carolina said. 
"No need to worry. We will." Dawn said.
Cynthia returned the Adamant and Lustrous Orb.
"I take it you no longer have the Griseous Orb Ash?" Carolina asked.
"Sorry." Ash apologized. "Giratina reclaimed it to use it's power to continue protecting it's dimension."
"I understand." Carolina nodded. "I suppose it's for the best given everything that transpired here. I shudder to think what would've happened if Team Galactic knew about it and took possession of Giratina."
"I find it ironic that we were able to witness the legend of time-space because of Team Galactic." Prof. Rowan said.
Ash stared at Saturn, Mars and Jupiter being led into a police van and walked over to it. He had some words for them. Dawn, Brock and Tomo followed him because they also had something to say. Cynthia and Looker did as well.
Right now they were placed in a police van. Saturn informed Jupiter that Cyrus had betrayed them and only considered them to be pawns. Jupiter was shocked to learn that.
"It's the end of Team Galactic." Saturn said calmly.
"You're right that it's the end of Team Galactic! Good riddance!" A voice shouted.
"Yeah, especially after everything you've done!" Another voice shouted.
It was Dawn and Tomo. The gang stared at them angrily along with Cynthia and Looker.
"Team Galactic." Cynthia said. "Your evil actions along with Cyrus's insane desire to create a new world nearly ruined this one and wiped out both humans and Pokemon. Thanks to these four good, brave kids you were defeated."
"You'll now pay for your sins in prison." Looker said.
Ash turned to Saturn.
"Since you witnessed us work alongside Azelf, Uxie, Mesprit and Giratina." He said. "It's like I told Jupiter before. Legendary Pokemon would never willingly work for evil individuals like you and Cyrus."
Jupiter was about to say something before Saturn stopped her. It was pointless protesting because Team Galactic was through.
"Have a nice stay in prison." Brock said.
"I hope we never encounter Team Galactic again." Dawn said.
"Don't worry." Looker said. "After everything they did, they'll be in jail for a while."
He thanked everyone for their help and left with the police to deal with Team Galactic.
Cynthia thanked the gang with all her heart for saving Sinnoh. Now that Team Galactic had been defeated, they could continue their journey in peace.
As for Jessie, James and Meowth
Jessie returned to Johto, James went back to Hoenn and Meowth went back to Christopher as they continued their new lives.