Swords and Secrets:

(Takes place during the Johto Saga)

(I own nothing from Pokemon or TMNT)

After being attacked by a mysterious group of Pokemon hunting ninjas, Ash, Misty, Brock and Persian all set out to help Officer Jenny catch them before they're able to hurt anyone else. Ash and Brock send out Noctowl and Golbat to patrol the area from the sky, while everyone else joins Officer Jenny in her jeep, searching for any sign of the enemy.

But while they were riding around, they were being watched by two more of said ninjas. But unlike the ones from before, these two were wearing a special type of suit that actually made them invisible. One of them then speaks into a communicator and reports back to his base commander:

"Master, we've located the target, but he's with the local authorities."

"Wait until he's alone, then you can proceed to take him. Then, report back to base when you do"

"Yes Master"

Per their given orders, the two ninjas proceed to follow our heroes, in camouflage mode of course. But rather than wait until anyone was alone, one of the ninjas went in one direction and made enough noise and commotion to attract the attention of our heroes. Then, when everyone was distracted, the other came up from behind and tossed several strange looking spheres. When they were under everyone's feet, each of the spheres releases a powerful electric jolt, ala Voltorb.

This was more than enough to stun everyone long enough for the other ninja to fire a stringy substance, very similar to Spinarak and Ariados' web, which wraps up everyone, human and Pokemon. And as everyone struggled to get free, the two ninjas regroup and practically disappear into the trees, with Ash in tow.

When they're gone, Persian manages to free himself and everyone else. Misty and Brock are both shocked about Ash being kidnapped and concerned about why he was kidnapped. But most importantly, worried about what will befall their friend.

Meanwhile, the leader of these Pokemon hunters, the Foot Clan as they call themselves, has just arrived at their Cliffside base by helicopter. Once there, he is given a fabulous and respected welcome, he is also soon greeted by the base commander:

"Oroku Saki, lord and master of the Foot Clan. I welcome you to my Base, my lord"

"Enough fanfare, Koran, I was told that our old friend, Ash Ketchum, has resurfaced and is apparently sticking his nose where doesn't belong"

"Indeed Master, I've dispatched two ninjas to follow and apprehend him"

"Excellent, then once they have him here, we can take care of things, as it were"

And with that, Koran bows in respect to his leader. But what none of the Foot ninja knew, was that the TR trio was nearby their base and saw Saki's helicopter as it came in. They started looking around, but eventually, they were spotted and the Foot sounded the alarm. Jessie and James panic, until Meowth finally tells them to run. But even though they manage to get far enough away before the guards show up, the same ninja who confronted them before walks up and says:

"I warned those clowns, Team Rocket is going to pay for this, big time!"

Meanwhile, back inside the base, Oroku Saki and Koran had watched the security cameras and saw what just happened. But their attention was drawn away when the doors behind them suddenly open. It was the same two ninjas that attacked our heroes earlier, and they still had Ash tow, tied up and now gagged. They then place him on his knees and present him before Saki himself. Saki then proceeds to talk to Ash as he removes his gag:

"Well, well, well, Ash Ketchum, it's been a long time"

Once the gag was off, Ash attempts to talk

"Hey, who do you think you…Hey how do you know my name?"

"(Chuckles) I should've known you wouldn't remember. But not to worry, we'll fix that soon enough"

As Saki attempts to pat Ash on his head, but the young trainer just pulls his head away in disgust.

"(Chuckles) Still as spunky as ever, I see. (Turns towards the two Foot Ninjas) Take him to the lab; we'll begin the procedure, right away"

And with that, the two ninjas pick Ash up and carry him off, with Saki and Koran following them. Meanwhile, Misty, Brock, Pikachu and Persian were searching desperately for any trace of the ninjas, hoping to find something that may lead them to Ash. Officer Jenny even called out her Arcanine to help with the search. But even with Arcanine's sense of smell, they still weren't finding anything.

Suddenly, Golbat and Noctowl return from their search and try to report what they found. Persian translates that they saw a strange looking helicopter with the Ninjas' symbol on it. They saw it heading for a nearby Cliffside, almost as if it were going to land. This was reason enough to investigate, especially if it meant finding and rescuing Ash. So the rest of the group followed Noctowl and Golbat as they led them to the cliff side.

Meanwhile, back at the Foot Clan base, Oroku Saki had Ash taken to the base's laboratory and placed in some sort of examination table. There, three scientists looked at him as he struggled to get free, all of them with facial expressions indicating that they were about to do something unpleasant, particularly the scientist who looked like he was the one in charge.

"Dr. Stockman, are you ready to proceed?"

"Indeed, Master Saki, I've done experiments on Ash before, I'll do it again. When I'm through, all he'll know is that he belongs to the Foot, now and forever"

After that, Stockman has his fellow scientists take Ash's hat off and place a technological looking headband on his head. Suddenly, Ash felt faint and slowly began to fall asleep. Then, he heard Oroku Saki begin to tell him a story about his life. He tells Ash that he was once a member of the Foot Clan organization and Right-hand man to Saki himself. Ash was a volunteer in a previous experiment of Stockman, where he was augmented by a secret serum that not only enhanced his natural abilities, but also gave some rather unnatural ones as well. What's more, it also gave him an evil streak.

When Ash heard this, he was both disgusted and ashamed. For so long, he's always considered himself a friend to Pokemon, but now, he finds that he was once their enemy. As Ash gave the facial expression of disgrace, Stockman removed the headband and had the other scientists remove him from the table. Then Saki walks over to Ash, pats him on the head and says:

"There, There, Ash, it won't matter. Like Stockman said, soon all you'll remember is that you belong to me!"

After that, Stockman and the other scientists drag Ash off and place him in a strange looking chair, almost like an electric chair. But before they could properly strap him in, one of the Foot Ninja came running in.

"Master, we have intruders, it's that pest, Officer Jenny"

"Is that so?"

"Yes and there's more, sir, she's with those people we found with Ketchum here"

That bit of information suddenly perked Ash up a bit, but Saki just smiles and says:

"So, a rescue is it, we can fix that"

Meanwhile, outside, Golbat and Noctowl had led Misty, Brock, Jenny, Pikachu and Persian to the exact Cliffside where they saw the helicopter fly towards. But just when they were about to look around for anything helpful, several Foot Ninja wearing camouflage suits appear out of nowhere and toss several of the shocking spheres from before, all around their feet. Then, before anyone knew it, they were all shocked and rendered unconscious. That's when Oroku Saki came onto the scene, but this time, he was in shadow and the silhouette he was casting gave the impression he was wearing some sort of suit. And all that was heard from him was a maniacal laugh.