Previously, in Pokémon: The Lost Child, Empoleon and Sceptile encountered a Pokémon falling from the sky. When they went to help it, they discovered it had amnesia. They tried to help it get its memory back, but Rayquaza attacked the newly revealed Deoxys. Deoxys defeated Rayquaza and flew away, warning Empoleon and Sceptile of the stakes beyond them.
Now Empoleon and Scpetile were left to continue on the journey, but while that was going on, another situation was brewing inside of The Brotherhood.
Aegislash sat sharpening his sword, preparing for the next assignment that would come at any time.
"Man, your life must be boring," Greninja said in the back, which Aegislash turned around to see.
"Oh, it's you again. What is it this time?" Aegislash asked.
"I was just checking by to see what was going on," Greninja said.
"Look, if you have some info on where Empoleon, Sceptile, or Zoroark is, then tell us," Aegislash said.
"You are hunting down Empoleon and Sceptile as well?" Greninja asked.
"Yeah, that is correct. They have both proven to be too much of a problem to be left alive," Aegislash responded.
"Where is your boss? I need to speak to him." Greninja asked.
"He is out doing something else. He won't be back for some time," Aegislash responded.
"That is unfortunate. I guess I will need to wait," Greninja responded.
"Ugh, as much as I don't like you, I guess you can stay here until he gets back," Aegislash said.
"I don't understand why you have been so hostile to me. We are both working for the same goal," Greninja responded.
"Just please leave me alone," Aegislash demanded.
"Alright, sheesh." Greninja leaves the area and heads to a different room in the base. Another member of the Brotherhood, Rapidash, overheard what was being said and decided to check up on Aegislash.
"Hey, Aegislash, what was up with that?"
"There is just something about him. He just showed up, giving us important information and asking for nothing in return. These are the kinds of signs that usually imply some sort of agenda, but I am just not sure what that is."
"He did say something about hanging around the place maybe you could try following him around and see what he is doing unless you have something else to do," Rapidash suggested.
"That is a pretty good idea. As of now, our hasn't assigned me anything."
"Just make sure to thank me if it ends up working," Rapisash commented.
"I will," Aegislash said.
Aegislash had his uncertainties over if this would work, but knew that he needed to at least give it a chance. This might be the best way to find out what is up with this Greninja.
Aegislash started following Greninja around the building. He spent most of his time looking around the various rooms, the one containing the control panel for the various operations of the Brotherhood, and the rooms where most of the members hung out. Most of them were getting ready for battle, with Darkrai's ultimate plan getting closer and closer, they were ready.
Greninja was starting to talk with some of the members.
"So what are you up to?" Greninja asked.
"Our leader's plan is coming. We are training for that day. Sorry, I don't recognize you. Are you a new member?" Magneton said.
"Yeah, I guess you could put it that way. I provided some useful information to Aegislash. Allow me to introduce myself. My name is Greninja.
"And mine is Magneton."
"So I am wondering, do you know what our leader's ultimate plan is? I wasn't told that," Greninja asked.
"We aren't sure exactly what it is. All we do know is that it is the day that we will finally control the entire world," Magneton responded.
"Do you have any idea when this plan is coming to fruition?" Greninja asked.
"Around 5 days," Magneton responded.
Aegislash was noticing how Greninja seemed very interested in what was going on with The Brotherhood. There could be multiple reasons for that, but it is still something that he found suspicious. After talking with some of the Pokémon for a bit longer, Greninja left the room to check out something else. Aegislash kept following Greninja. This time, Greninja went inside the lab where most of the experiments happened.
Greninja spent a few minutes just looking around. However, when he came across a control panel, Greninja immediately jumped on it and started accessing it. This act confused Aegislash. How could Greninja already know this so well and who would he be accessing the control panel? Aegislash was a decent distance away though, so he couldn't tell what Greninja was doing on it.
Aegislash snuck around some of the objects, trying to be as quiet as possible, and Greninja didn't see or hear him doing so. Aegislash had gotten pretty good at sneaking around, so that was probably helping with this. Aegislash was able to get a better look at what Greninja was doing, and it seemed he was trying to learn more about The Brotherhood.
"This one is invested in exactly what this place is like and what our ultimate plan is. What could be your motive for that, Greninja?" Aegislash wondered.
Aegislash took a closer look at exactly what Greninja was doing. He was having a really hard time seeing what was going on. However, Aegislash was eventually able to get a much better look at what was going on. Greninja seemed to be trying to get inside of the system. He was straight up hacking his way inside. Aegislash thought that his suspicions were confirmed right here, so he jumped out and launched a shadow ball at Greninja.
Greninja got hit by it and was instantly sent back. Greninja looked to see what he got hit by and saw Aegislash. His first response was to ask, "Aegislash, what is going on?"
"I saw you trying to hack into our system. You are up to something. I can feel it. It's a good thing I caught you before you did any damage," Aegislash responded.
"Wait, hold up. You have this all wrong. I spotted a flaw in your security and was trying to fix it myself. Go check what I have been doing if you don't believe me," Greninja responded.
Aegislash was skeptical, but on the off chance that he was wrong, he decided to check up to make sure. He kept a close eye on Greninja to make sure that they didn't leave while he was distracted. Aegislash was eventually able to finish checking and reported, in an annoyed tone, "You seem to be telling the truth."
"See, I told you. Maybe you should take a chill pill, man. I am only here to help."
Aegislash ignored the comment and floated away in annoyance. Aegislash could not get rid of the feeling that something wasn't right, but he had no way of proving it. Aegislash went back to his main place, where he found Rapidash still chilling.
"So Aegislash, how did it go?"
"I thought I had something, but it turned out to be nothing. Something still feels wrong about this Greninja, but I can't prove anything. Do you have any idea how frustrating this is?"
"I do understand how you feel. Look, Aegislash. We have been friends in The Brotherhood for as long as I can remember. If you feel that there is something that isn't right, I do not doubt that you are correct about this," Rapidash responded.
"Those are the words I needed, Rapidash. I will keep going until I can uncover the truth." However, while Aegislash was talking, his communicator started ringing. He checked to see what it was and noticed that it was Darkrai. Aegislash had to answer, so he did exactly that.
"Aegislash, there is a situation I need you to look at," Darkrai said.
"What is it, master?" Aegislash asked.
"There is some sort of problem with our mining volcano none of the members stationed there have been online for days, I need you to check out what is going on," Darkrai responded.
"I will do that," Aegislash said, afterwards hanging up and saying to Rapidash, "Looks like that will have to wait. I have more important business to take care of."
However, meanwhile, with Greninja, "That annoying Aegislash. He is the only one that even suspects anything though I have everyone fooled. Thanks to him I know have everything I need," Greninja while saying that gave a smile.