A Pokemon Adventure!

Part 1; Chapter 5: Plucking the weeds.

Wyatt woke up to a big thud. He looked around and didn't see anything. Thud! He heard it again. Wyatt stood up. Then he noticed that Tot and Bruce were gone. Shoot, Wyatt thought. He searched around frantically and still they were nowhere in sight. Thud! Wyatt looked through some trees and saw Tot spray some water into the air. Wyatt was confused as to why he did that. Just then, Bruce zoomed down into the ground. Thud!
Oh, they must be training. Wyatt thought. He walked over to them and tried to see how they were doing. When he got a better view, he saw exactly what was happening. Bruce was tackling down at Tot, and Totodile was using water gun to fight back.
"I hope this is just training!" Wyatt yelled. After saying this, Tot looked over and ran towards me.
"Totodile!" He yelled. Bruce flew down next to him and cooed. I pat both of them on the head, praising them for their training. When suddenly, we heard some people talking.
"Thi- -ake us ri-." One voice said. I could barely understand it so I got closer. Another, deeper voice says
"We're going to make a killing off of selling this pokemon." This confused Wyatt. Selling Pokemon is a crime! By now, Tot and Bruce have walked up next to Wyatt. Wyatt whispers to Bruce,
"Bruce, fly up. We can't see what they are doing through these bushes. If it's something bad, coo once. If it's something good that we shouldn't mess with, coo twice." Bruce nodded, seemingly understanding Wyatt. He flew up into the sky. After about a minute, Bruce flew back down and cooed once. "Something we should mess with, got it. Ok guys, on three. One. Two. Three!"
When Wyatt finished saying that, all three of them ran through the bushes. They saw two people, both wearing the same hooded outfit. Near them was a cage, that appeared to have a pokemon inside.
"What the!?" One of the people say.
"Totodile Use bite!" Wyatt yells. Totodile jumps toward one of the men and bites his arm. His jaw locks on to his arm.
"Bruce, peck the other one!" Bruce relentlessly pecks at the other guy. While the two men are distracted, Wyatt tries to figure out what the cage was trying to keep inside. He saw what looked to be a ralts. Don't worry, I'll get you out of there. He thought. He noticed a symbol on the cage. It was in the shape of a tree sapling. Looking at the hooded people, they had small versions of the emblem on their chest. What are these guys, a cult or something? Wyatt thought.
"Totodile! Help me out here!" Totodile, who was still on the hooded figures arm. The figure was on the floor, unconscious from blood loss. Bruce chased the other one away.   Totodile waddled up to where Wyatt was standing. "Think your jaws are tough enough to break through this cage?"
"Dile!" He yelled in response. He put his teeth on the cage and bit down, breaking it almost instantly. Wyatt looked back into the cage. The Ralts appeared to be unconscious. Wyatt picked it up and carried it out of the cage. When they were in the sun, Wyatt, Tot, and Bruce realized that they were not an ordinary Ralts. What would normally be green on a Ralts is instead...purple?