When Ryder was finally incapacitated, Officer Jenny called in the police to arrest all the Team Rocket members and Pokémon as well as Ryder. Luckily, the Pokémon still had their power inhibitors in their ears, so they were easy to recall to their Poke balls, which Flynn and the others brought when they left Ryder’s lab.
Bayleef, who had wanted to keep her human body longer, saw that her Pokémon body was being led away and ran up to the policemen to explain the situation. They were skeptical at first, but eventually they believed her and used Flynn’s machine to swap them back, much to Bayleef’s dismay.
Before the Pokémon and humans associated with Team Rocket were hauled away in trucks, Ash approached Lily and asked, “Hey, why’d you help us out? Was it because you—”
“Don’t try to read too much into it,” Lily said arrogantly. “Ryder was going to betray Team Rocket, so I put an end to the threat. Nothing more.”
After that, the Pokémon and human members of Team Rocket were hauled away with Ryder to a prison outside the Indigo Plateau.
“Now that that whack-job is locked away, I think I’ll take my leave,” Haunter said as he started to fly away.
“Wait, where are you going to go?” Ash asked.
“Doesn’t matter. I’m sure I can give at least a few people the creeps wherever I go. That’ll be the sweetest music to my ears. Later.” And with that, Haunter flew away.
Beauty and Patty approached May and Dawn. Beauty said, “Please forgive us for stealing your bodies. We didn’t know what Ryder was planning would be harmful.”
May said, “I know you didn’t. The important thing is that you did try to help us in the end. I can forgive you and Patty after that.”
Patty jumped up on May’s shoulder and asked, “Really? You aren’t mad at Mommy and me?”
Dawn smiled and said, “Of course not. We know you didn’t mean any harm.”
Patty turned to face Beauty and said, “They aren’t mad! Isn’t that great, Mommy?”
Beauty got a happy expression on her face and said, “It sure is. Now, come on. We need to find a place to call home.”
Patty started to tear up when she asked, “We’re leaving, Mommy?”
“You don’t have to,” Delia said, approaching the two Pokémon. “You can both stay with me, if you’d like.”
Mimey walked up next to her and said, “Yeah, you should stay with us. I’ve always wanted more Pokémon around to talk to on a regular basis.”
Excited at the opportunity, Beauty nodded her head and said, “Thank you, Ms. Ketchum.”
“Please, you can call me Delia.”
Emmy watched the two out of the corner of her eye, then started walking into the forest. Iris noticed this and said, “Hey, Emmy; where are you going?”
“I don’t know,” Emmy said, a depressed tone in her voice. “I guess I’ll try to find my family. Just knowing they’re doing fine will be a great comfort to me.”
In response, Iris extended her hand and said, “Well, why don’t you join me? I love traveling, and there are many trainers in the world. We can find your family together.”
Emmy turned to Iris and asked, “But you already—”
“I know I already have an Emolga, but she won’t mind a new friend. Don’t worry; we’re friends now, right? I’ll make sure you’re well taken care of.”
Emmy got teary-eyed and flew in Iris’ hair, popped out with a smile and said, “Thanks, Iris.”
Meanwhile, Flynn stood with Ditto facing Professor Oak and the other girls who had been turned into Human Pokémon. “I’m sincerely sorry this had to happen to you!” Flynn said in an apologetic tone. “I didn’t know Ryder would betray me. I assure you, my experiments and machines were meant to improve our relationships with Pokémon.”
Professor Oak approached Flynn and said, “Flynn, there’s nothing for you to apologize for.”
“But…but what about—”
“You were a victim, just like the rest of us,” Cynthia said, stepping forward. “Ryder was the one behind this mess, not you. There’s nothing for you to be upset about. You can still carry on your research in the relationship between humans and Pokémon.”
Flynn gave Cynthia a distant stare and said, “Still, there is one thing I’d like to do before moving on.”
(2 days later)
Flynn and Ditto led Professor Oak, Ash, Pikachu and Bayleef, who insisted on going with Ash, into their old lab in Cerulean City. Looking around, they expected the place to be filled with dust and cobwebs, yet found it being cleaned spotless. Not taking the time to wonder how it was kept clean, Flynn approached the machine in the center of the room.
“Is that the first body-swap machine you created?” Ash asked.
“It is,” Flynn said in a melancholic voice. “This is what caused you and your friends so much misery.”
“Hey, it wasn’t your fault,” Ash told Flynn. Pikachu and Bayleef nodded their heads in agreement, having left their translation collars back at Pallet Town.
“I was still the one who created it,” Flynn shot back. “I wanted to use this machine to understand how the relationship between Pokémon and Humans looked like from the point of view of the Pokémon. Instead, it almost caused a world takeover by one of my closest friends. I can’t let this go unabated.”
“What are you planning to do?” Professor Oak asked.
“I’m going to dismantle this machine,” Flynn said, resolved. “I can’t allow anyone else to abuse the power this machine possesses.”
Before Flynn could make a move to act on his impulse, the doors to the lab opened up and allowed a small group of children and Pokémon into the lab. It consisted of a small girl and her Vulpix, a wealthy-looking boy with a Poochyena, a glasses-wearing boy and a Pichu and a slightly older boy with a Machop.
Shortly after their arrival, a teenage girl approached the small group and said, “Kids, how many time have I told you not to get near the…wait! Mr. Flynn, is that you?”
“What are you all doing here?” Flynn asked, surprised at the interruption.
The Machop looked up and immediately ran to Flynn, saying, “Machop! Machop, chop, Ma, Machop!”
“What are you—”
“He just said, ‘Welcome back; Machop and I missed you!’” Ditto said, surprised at what the Machop just said.
The girl walked forward and bowed apologetically. “I’m sorry, Mr. Flynn. When I wasn’t looking one day, these kids wandered into your lab and got their bodies switched with their Pokémon. I’ve been looking after them after explaining everything to their parents, but now that you’re back, I was hoping you could switch them back!”
Flynn stared at the kids and Pokémon at his feet and said, “I’m sorry you had to suffer like that. I’ll get you fixed right aw—”
(“This was so much! Can I do it again?”) The Vulpix said, with the little girl next to her agreeing.
The kids happily told Flynn, through Ditto and the Pokémon now in their bodies, about how they loved playing with their Pokémon while in each other’s bodies. They had gotten a deeper relationship with their Pokémon because of the experience and the teenage girl, named Bay, looked after the kids and Pokémon with a caring attitude.
Flynn stood amazed at what he had heard. Professor Oak walked up next to him and said, “It seems like there’s some good that can come from your machines yet.”
“But…but what about the—”
“Flynn, your machine has the potential to do great good as well as great evil. It all depends on the one who uses it. Judging from the reactions of these children, I’d say there is potential in this machine for your research.”
“Flynn, why don’t you move your lab to mine? I know you have great ideas and a kind heart; you just need the proper way to put them to use. I think there’s a place in this machine in my lectures, actually, in order to offer the children a first-hand experience of my lectures; plus this could help strengthen relationships between people who aren’t trainers and their Pokémon.”
Flynn looked off into space as he thought aloud, “Well, I don’t suppose allowing children will lead to world-wide disaster.”
After another brief moment in thought, Flynn said, “Okay, I’m going to switch you all back to normal, then I’m going to be moving to Pallet Town.”
The kids and Pokémon jumped up and down with excitement. The Vulpix, which now had the body of a little girl, turned to Bay and said, “We’re going to be back to normal soon! Aren’t you excited?”
Bay smiled and said, “Yeah, it is exciting. Honestly, I wish I could live like a Pokémon for a day.”
(At Pallet Town; 3 days later)
Ash looked at the line of children and trainers that were hoping to be able to switch bodies with their Pokémon. The ones who were interested in Contests were going to try to show their Pokémon how to perform the moves they were hoping for while the other trainers were going to try to figure out a training regimen that their Pokémon could follow.
Flynn, for his part, oversaw the entire process and was able to see the good his machine was able to produce when used by the proper people with the right intentions. Professor Oak also took children who had swapped with Pokémon to the area out back where the Pokémon of other trainers were staying. The children would then spend their time getting to know about Pokémon on a more intimate level by having the Pokémon themselves tell them about the strengths and weaknesses of each Pokémon.
Ash also took one last look at his house, where Patty and Beauty started to adapt to their new lives with his mother and Mimey. Seeing everything seemed right, Ash looked at Pikachu on his shoulder and asked, “Okay, buddy, you ready for another training trip?”
“Pika, Pi!” Pikachu said, no longer wearing a translation collar. Ash tried not to let the language barrier prevent him from understanding the feelings of his Pokémon, so opted for Pikachu to return the translation collar.
“Okay, then let’s—”
Ash turned around to see Bay running toward him, a distressed look on her face. Bay had helped Flynn move his equipment to Professor Oak’s lab and, from what Ash had heard, was going to be heading back to Cerulean City the next day.
“Bay, what are you—” Ash started to say, but was rendered silent as Bay trapped Ash in a tight hug.
“Please, take me with you! Don’t leave me back here again!!”
“What are you talking about?”
At that moment, Flynn and Ash’s Bayleef came running up to Ash and Bay in a panic. “There you are!” Flynn said to Bay before turning to Ash. “Ash, I’m sorry, but Bay wanted to know what it was like to be a Pokémon and your Bayleef volunteered. Before I knew it—”
“I can figure out the rest,” Ash said, realizing the Bay hugging him right now was really his Bayleef in Bay’s body.
(“Bayleef, why’d you run off?”) Bay asked, speaking Bayleef’s language. (“I’m not upset, but I’d like to know.”)
“I’m sorry,” Bayleef told Bay, “but I had a feeling Ash was about to leave again and I had to tell him something.”
“What is it?” Ash said, causing Bayleef to turn to him again.
“Ash, I want to be a part of your next training trip! I know you like making new friends, and the new friends you pick up in the different regions are really nice, but I can’t help but feel a little neglected. I want to be able to share adventures and memories with you again, like we did in Johto! Please don’t leave me behind again!”
Ash was taken aback after hearing Bayleef’s words. He also knew that Bayleef had a valid point. He had only ever taken Pikachu to every new region he’s adventured through. With a sympathetic smile, Ash told Bayleef, “I’m sorry I made you feel that way, Bayleef. If you want, I can take you along with me. However, I’d like you to be in your own body for this.”
Excited at this news, Bayleef told Ash, “Thank you!”
Finally, an hour later, Ash stood on the path that led out of Pallet Town. He shot a glance at Pikachu, riding on his shoulder, then turned to Bayleef, back in her own body and standing next to him.
With a final confident grin, Ash said, “Okay, you two, let’s get going!”