A/N: Once again, this was the longest project I have EVER done, at the time I wrote it.

Last Time on Pokemon World War: Ted's group finally reached Mahogany Town. They noticed the strange light show and fixed it by capturing a crazed Deoxys. Everyone also learned about the escape of Team Rocket's Cyborg Ninja. Despite the danger, Zora and Matt decided to lead a group to find it somewhere to the east. Ted and Alex continued their march to Olivine bay, where The Rocket Navy was poised to attack.


Chapter 29

As Matt and Zora's Team emerged from Mt Mortar 4 weeks after leaving Mahogany Town, there was a somber feeling throughout the team. They didn't get lost or ambushed. They simply had to slow it down for those not used to wandering around in the dark. They were now finally entering Mahogany Town. "Whew, we finally got here." Said Kris. "I can't wait to investigate this Super Solider!"

"We'd best be on our guard." Said Zora. "This town is crawling with Rockets. Even though they're taking the blame for what happened here, they might still try to attack us."

"We're not just gonna try." Said a Rocket Commander nearby. "We're going to destroy you all!" Several Rockets then swarmed the area. They were members of Ash's personal assassins. They soon had the perimeter sealed off.

"How do you suppose we escape from this one?" Asked Tom.

"Leave it to me!" Said Terra. She then brought out Kadabra. "Use Teleport!" the group was then teleported to another part of town. Soon afterwards there was an explosion. "I left them a little parting gift." Terra explained.

"Great work." Said Monica. "We're right in front of where that lab used to be, by the way." Indeed they were. Although the fires had long since been extinguished the place looked nothing like a building. It was like trying to dig your way through a scrap yard.

"What are we possibly going to find in here?" asked Hiro. "This place is a mess!"

"That's why we're looking in here." Said Matt. "Maybe we'll find something useful the Rockets missed." After digging for a while, it seemed like their attempts to find clues was in vain. That was until Taylor found a black box. It was close to where the rear of the building would have been.

"I wonder what's inside this thing?" asked Matt.

"Only one way to find out." Said Monica. When they opened it they were shocked at what they saw. Inside the box they found documents and pictures of Jordan McArthur. Some of the documents included a birth certificate and a death certificate.

"It seems Jordan was here recently." Said Hiro. "Now we know what became of him after the Rockets sprung him from prison."

"The question is why?" asked Kris.

"That is something we must find out." Said Hiro. "We'd better go to Blackthorn City and find out."

"I agree." Said Matt. "We've been here long enough, anyway." After exiting the ruined lab they headed eastward into the Ice Cave. Unlike The Union Canyon The Ice Cave had not been altered by the Rockets. The high-leveled Ice and Ground types that lived there prevented that from happening. There were signs that the Rockets were in the cave, however. They could see floodlights and tire tracks.

"Looks like there's a Rocket brigade using this cave to reach Blackthorn." Said Zora. "We may even run into them."

"Let's be careful, then." Said Tom. "I don't like surprise attacks." As they continued, they came upon a wild Sneasel. Upon seeing them it ran down a passageway.

"Looks like the pokemon here are scared of us." Said Terra.

"No, it's something else." Said Monica. "There is danger nearby."

"How Close?" Asked Matt.

"Very close." She replied. "This way!" She led them down the same corridor they saw the Sneasel go. Inside they saw tire tracks. It seems the Rockets had come this way too.

"I wonder what's going on?" Asked Kris. "Every time we find something we discover a dead end."

"We'll find what we're looking for soon enough." Said Zora. "We should stay together in this room. We might break through the floors here." Right after saying that, the whole team fell through a hole to the cavern below. It was not a pleasant experience for everyone. When they found out what they fell into they were startled. The room was littered with corpses—the corpses of Rockets to be exact!

"What's this pile of corpses…!" exclaimed Terra.

"I don't know what did this, but whatever it was is close by." Said Monica.

"You don't think it was that Super Solider, do you?" Asked Hiro. "If so, then he is near us." They then heard the sound of gunfire coming from the a nearby passage next to them. They hurried into the cavern. Inside they saw a heavily armed Rocket Brigade shooting at something invisible to the naked eye. Whatever it was that was attacking was apparently moving too fast for them to hit it. The Rockets were all felled one by one.

As the creature made its way towards the exit the Rockets kept on firing. The unseen figure disposed of them with ease. "What is that...?" asked Matt.

"The one we seek." Said Zora.

"Do you see it?" Asked Terra. "I've never seen anything move so fast!"

"At least you can see it." Said Tom.

"Let's get closer!" Said Hiro. They quickly ran up the path after the Super Solider. When they came to the exit to Blackthorn City they saw a Rocket being impaled in the air by something. It then made itself visible.

"It's…not…human…" said the Rocket.

"No thanks to you!" Said the Cyborg Ninja. It then smashed the man against one of the icy walls of the cave. The force was fatal. The Cyborg then walked out of the cave as if nothing had happened.

"I've never seen anything like that!" Said Taylor. "I don't know if any of us can take that thing!"

"Well, we have to try." Said Matt. "If we don't stop him there could be trouble!" They hurried after The Ninja, knowing they could all be slaughtered. When they came out the cave they saw The Ninja pointing its blade at a shady guy standing next to a sign. The man didn't seem worried at all.

"Where is my friend?" The Ninja asked him. "You told me he would be here."

"I've already told you." The man said. "I can't tell you when he'll come!"

"Don't Move!" Said Matt, pointing a handgun at the Cyborg Ninja. The Ninja turned around at this.

"Ah, finally!" Said the Ninja. "I've been waiting for you, Matthew Oak. Now you and I will have a fight to the death. You will kill me or I will kill you. It makes no difference."

"What, is it revenge?" Asked Matt.

"It is nothing so obvious as revenge." Replied the Ninja. "Only in this can my soul be at peace." The shady guy then backed towards Blackthorn City.

"I'll stand over here if you don't mind!" He said.

"Fine, you can watch from there." Said the Cyborg.

"You might want to stop threatening people like that!" Said Matt.

"Now, make me feel it!" Said the Ninja. "Make me feel alive again!" The two then locked in a bitter and raw battle, using only their fists as weapons. It went on for several hours, each matching the other move for move. During this pure and brutal fight, the name of one person came to the mind of Matt. After fighting some more, Matt kicked The Ninja into an old building, demolishing it. Everyone was surprised when it emerged from the building as if nothing happened.

"Ah, I felt that Matt." Said the Ninja. "Do you remember me now?"

"It can't be!" Matt exclaimed. "You were killed in Kanto…" The Cyborg then collapsed to the ground. It seems it had run out of energy.

"What happened?" Asked Monica.

"Seems he's run out of power again." Said the Shady Guy.

"You know Jordan?" Hiro asked him.

"Of course." Said the man. "It's because of me he at least knows what his name was."

"Who are you?" Zora asked him.

"My name is Dr. Ken Baker." The man said.

"WHAT?!" She exclaimed. Apparently she knew this man.

"I was the lead scientist that helped to make Jordan what he is today." He continued. "As you may have heard on the news, he was created solely to exterminate the ex-members of Team Rocket. Although I knew this I went along with it anyway."

"You monster!" Said Taylor, picking Ken up and holding him in the air. "All of those people did the greatest thing ever by quitting Team Rocket! All of them have worked really hard to put that behind them."

"Hey, take it easy!" Ken exclaimed. "This story gets better!" Taylor slowly put him down. "You see, I was feeling really bad about Jordan one day having to kill Kaylie. I have a crush on her, you see. Even when I found out she was pregnant with Alex's kid I still was in love with her."

"Did you ever tell her?" Asked Kris.

"I was going to but then she suddenly left for Kanto." Ken replied. "I was crushed. Then a couple weeks later we got word Kanto had been liberated by a small band of freedom fighters. When Ash got word Jessie, James and Jordan were in jail awaiting trial he decided to break them out. We just didn't expect it to be so heavily fortified. They were able to hold onto Jessie and James and Jordan was fatally wounded. They brought his body back, anyway."

"What did you plan to get from a corpse?" Hiro asked.

"A lot, actually." Said Ken. "After we revived it, of course. After doing that we fitted him with an exoskeleton. We kept him drugged these past few weeks and used him to test many different kinds of gene therapy techniques."

"That's the sickest thing I've ever heard!" Zora exclaimed, remembering her own past. "Seriously, how the fuck can you live with yourself after what you did?"

"I already know I'm going to hell." Ken replied, shrugging. "At least Jordan was already dead when it started…" Unable listen to any more, Zora ran into Blackthorn City.

"Zora, wait!" Said Taylor.

"Follow her." Said Matt. "You too, Kris."

"Gee, what's with her?" Asked Ken. "I though she wasn't supposed to take after—"

"You don't know?" Asked Matt, grabbing Ken by his shirt. This caught him off guard and he almost fell flat on his rear. Disgusted by this, Matt helped him on his way down.

"Zora is Giovanni's daughter." He said, looking him right in the eye. "She was abused and tortured by Team Rocket her entire life. Even when her brother took over that didn't make things any better for her. In fact, it made things worse. I really hope you can look at yourself in the mirror after this. Team Rocket has fucked up the lives of so many people and pokemon and YOU my friend, are the only one who's actually felt any remorse!"

"That's why we left." Said Ken. "A few months ago I made some changes to Saul's programming. I give him his identity as Jordan again. I also managed to cut everyone Saul had been originally programmed to kill from his memory."

"If that's true, why did he try to kill me?" Asked Matt.

"Saul told me he wanted to settle an old score with you." Ken replied. "I couldn't do anything about that."

"Ha, sounds like him alright." Said Matt after picking Ken up from the ground.

"So how did you two end up here?" Asked Monica.

"I set Saul's programming so he would be 25% good." Said Ken "When Ash found out he tried to kill me. Fortunately the changes I made gave Saul the courage to fight back at Ash. After that we destroyed the lab, making sure no one could ever do it again. We've been hiding out in Blackthorn City ever since."

"That's something alright." Said Hiro. "But it still doesn't excuse what you did!"

"I know, I know!" Said Ken.

"I'm sure that if you were the scientist who forever changed Zora's life, she wouldn't hesitate to kill you." Said Monica. "Wait—didn't she recognize you?"

"Now that you mention it…" said Ken.

"What the hell!" Said Tom, pointing his weapon at Ken's head.

"If you kill me, no one will be able to stop Jordan." Said Ken, quite calmly. Tom lowered his weapon. "That's better."

"What is it you want from us?" Asked Hiro.

"Jordan wanted to fight Matt." Said Ken. "As for me, I want to help you destroy something that could destroy the world. For the last 10 years Team Rocket has been working on combining the cells of Mewtwo, Lugia, Ho-Oh, Kyogre, Groudon and Rayquaza. Now they have finally succeeded. Deep in an underground bunker in Goldenrod City it sleeps. Ash is waiting for Ted to arrive so he can activate it."

"Have you ever seen this behemoth?" Asked Terra.

"No, but I hear it has no weakness to any pokemon type and could easily alter the face of the planet." Ken replied, shrugging. "It is the ultimate bio weapon. Not only that, it's been patented so it can't be caught even with the Master Ball. I don't think even Ted can stop it."

"I see where you're going with this." Said Matt. "You want Saul to help us."

"If he'll cooperate, that is." Said Ken.


After going into Blackthorn City Ken recharged Jordan's exoskeleton. They also learned from Taylor and Kris that Zora went to the Dragon's Den. Ken decided to talk to her. He quickly found her and opened with an apology. He considered Zora breaking his nose a peace offering.

"I haven't the slightest idea why I'm letting you live." She said. "After what you've done, you shouldn't even have that luxury. Maybe it's my father's genes."

"Or it could be that you're pregnant." Ken replied replied, shrugging.

"How did you know that?" She asked in surrprise. "Not even Monica knows and she can read minds."

"I delivered you and Ash." He replied. "That and I do have a wife and kids of my own."

"If you tell anyone before I do I will execute you." She said, holding him above her with one hand.

"Got it." He wheezed. A few hours later, Jordan woke up. It wasn't the reception even Ken had expected. Jordan leapt out of the building and ran off to the west. He jumped on a Charizard and it flew from sight.

"I wonder where he's going?" Asked Terra.

"Our next destination, of course." Said Hiro. "National Park. From there we'll link up with Ted's team and go onwards to Goldenrod City."

"Let me come with you." Said Ken. "I can help by unlocking very difficult security locks. I also know the place well."

"Sounds like a plan." Said Matt. Zora made no reaction. Matt could only assume it to be her way of accepting the fact that she'd have to let him live.

"Wait, Kris!" Said Clair as she ran from her Gym. "You completed your training and now you receive this Scale Fossil as proof."

"Wow, thank you!" She replied.

"If you know someone who revives fossils, you've got yourself a Red Gyarados." Clair explained with a smile.

"Will do." Kris replied. The group then headed back west for the big dance.


This is the 29th straight chapter that has added plot. More easter eggs from Metal Gear Solid here but it's way more obvious.

There's 5 chapters remaining. That can be certain. Next chapter we see what Ted's group is doing…