Previously in Pokémon: The Lost Child. After getting an ominous warning from Deoxys, Empoleon and Sceptile faced off with their old foe, Dark Empoleon. It was a long and gruelling battle that they had with him, but they were eventually able to come out on top, with some help from Zoroark and Deoxys. In the end, Deoxys left the trio with another ominous message, and soon the final confrontation with the mysterious evil Brotherhood would finally begin.
Empoleon and Sceptile were sitting around wondering where to go next. They knew something massive was coming and didn't know how to handle it.
"Hey Sceptile, there has been something on my mind," Empoleon commented.
"What is it?" Sceptile responded.
"Like, I know that the Brotherhood is bad, but what is their gameplay, you know, like the ultimate goal that they are working towards?" Empoleon said.
"That is a really good question. I can't say that either of us knows that it could be something as simple as world domination or making money," Sceptile said.
"That is fair, just a question that has been nagging at me for the longest time," Empoleon responded.
While Empoleon and Sceptile were hanging around the place, Zoroark came back to them. She jumped out right in front of them and said, "Hello again."
"Zoroark, where did you go?" Sceptile asked.
"That isn't important. What is important is that I have finally found the location of the Brotherhood's base."
"How did you manage to do that?" Empoleon asked.
"As of now, I can't explain. I can't take them down myself, I need your help," Zoroark responded.
"I don't like how secretive you are being, Zoroark. We are willing to help, but if this is going to go well, we need to know everything," Sceptile said.
"I understand why you feel that way, but the truth is you can't know, I mustn't say anything for my plan to work," Zoroark responded.
"I am willing to trust her Sceptile. Zoroark has done a lot for us," Empoleon said.
"Yeah, I remember our first meeting not too long ago."
"I will try and trust you on this, Zoroark. You have indeed done a lot for us," Sceptile reluctantly said.
With that, Zoroark would lead Empoleon and Sceptile to The Brotherhood's base, which was relatively close by, so they got there quickly. When they got there, all they saw was a mountain. Sceptile and Empoleon were both confused, and all that Sceptile could ask was, "What are we doing here?"
"Hide behind these bushes and you will see what I mean." Empoleon and Sceptile took Zoroark's advice and hid behind the bushes with her. After a few minutes, they saw a Skarmory fly towards the mountain, used a panel, and activated a secret code that opened a disguised door.
"That is the base of the Brotherhood. Let's hurray inside before it closes," Zoroark said. The three then headed inside just before the door closed. They were now inside the base of the Brotherhood.
"This is what the base of their place looks like," Empoleon commented.
"Yeah, we need to be very careful though as to not get spotted."
"Hey Zoroark, There is one question I have been meaning to ask. What do you plan to do while we are here?" Sceptile asked.
"The biggest thing is that we need to figure out what they are planning. I have managed to gleam that they are plotting some kind of world domination, but I am unsure how they are going to accomplish it," Zoroark said.
"That is a question I was wondering about recently," Empoleon commented.
The trio goes around The Brotherhood base trying to avoid getting spotted by the various members of The Brotherhood. The Brotherhood had far more members than what they saw coming. It concerned them slightly. After going around The Brotherhood's place, they got to a place where they spotted Aegislash. Empoleon and Sceptile quickly hid under a table so that they wouldn't get caught by Aegislash.
While he was hanging around, Aegislash didn't see them. They heard him say, "Where is Greninja? I expected to see them around."
Greninja showed up from out of nowhere and said, "I am right here, Aegislash."
"Where have you been?" Aegislash asked.
"I had to take care of some personal matters." Greninja replied, "I have some more useful information for you. Follow me and I will tell you everything."
Aegislash and Greninja left to head to a different room, with Aegislash not knowing that Empoleon and Sceptile were in the room. Empoleon and Sceptile got out of their hiding spots, with Empoleon commenting, "Phew, that was a close one."
"I know, right? Anyway, Zoroark, we need to keep moving," after saying that Sceptile got no response.
"Um, Zoroark? Are you there?" Empoleon got no response to that.
"That is weird. She was here only a minute ago," Sceptile commented.
"What if she is in trouble?" Empoleon wondered.
"That is the same worry I have. I hope that isn't the case. We need her to help take down the Brotherhood," Sceptile said.
"What should we do now, Sceptile? Now that we don't have Zoroark to help?" Empoleon asked.
"I don't know, maybe we could check to see if there is any useful information."
"Where could we possibly find anything useful to use?" Sceptile wondered.
"Hey, Sceptile, look over there," Empoleon said, pointing to a room.
"It looks like some kind of control room, I guess we could take a look inside. There might be something useful," Sceptile responded. Empoleon and Sceptile went into that room. It was some sort of control room that was handling the operations of the entire Brotherhood.
"Sceptile, take a look at this," Empoleon said while pointing at a control panel.
Sceptile came over to check it out and, after looking at it, said, "This is interesting. I will take a look inside." Sceptile starts messing around with the control panel and manages to get inside, commenting, "That is weird. There is no kind of protection on this thing. I feel like The Brotherhood would have better security."
"What have you found?" Empoleon asked.
"Give me a bit, I am still looking through this," Sceptile kept looking through the control panel while also commenting, "Man, this has a lot of info."
"Something doesn't feel right about this," Empoleon commented.
Sceptile discovers something on the control panel and instantly reacts with dread. Empoleon notices and asks, "What is wrong Scpeitle?"
"The Brotherhood's plan is worse than we could have imagined. Darkrai has some sort of device that will enable him to spread his nightmares across the entire world, trapping everyone in an eternal nightmare and allowing him to rule over the world," Sceptile explained.
"Wait, what!" Empoleon said he was in complete shock to learn this.
However, before the two had time to do anything with this information, several members of the Brotherhood attacked them, those being Aegislash, Rapidash, Magneton, and Scizor. Aegislash afterwards comments, "It looks like that Greninja's tip paid off after all."
"I fear we may have fallen into a trap, Empoleon," Sceptile commented.
"What are you talking about? I never set any kind of trap." Aegislash asked.
"You must have unlocked this control panel to lure us to this location," Sceptile commented.
"What are you talking about? I did no such thing," Aegislash responded.
"We now know everything about what The Brotherhood is planning for Aegislash," Empoleon explains.
"Well, in that case, you two are not leaving this place alive," Aegislash commented.
Empoleon and Sceptile got into a battle with the four. Empoleon fired a hydro pump at Rapidash while Rapidash fired a flamethrower to try and clash with it. Sceptile took on both Scizor and Aegislash in a direct fight, but he is getting overwhelmed quickly by having to take on both. Magneton starts firing shock waves at Empoleon, which Empoleon tries to dodge out of the way, but is having trouble keeping up with Aegislash. Sceptile backs up and tries to hit Aegislash and Scizor with a dragon pulse, but the move barely does any damage to them and they come back to tack on Sceptile more.
Empoleon and Sceptile put up the best fight that they could, but they were no match for four members of the Brotherhood at once, and they quickly got overwhelmed and knocked to the ground.
"Darkrai will be very pleased to see this," Aegislash comments. Aegislash then takes Empoleon and Sceptile over to Darkrai's place and shows them to him while saying, "Master, I managed to capture these two."
"It looks like my tip paid off for you," Greninja commented, who was next to Darkrai.
"I don't understand what happened," Sceptile said.
"Very good job, Greninja and Aegislash. Now you two, why don't you tell me where your little friend Zoroark is, I know that she came with you," Darkrai demanded.
"We don't know where she is and even if we did, we aren't telling you a thing," Empoleon responded.
"Very well. Scizor, take these two to be prepared for execution," Empoleon and Sceptile felt a wave of dread from what Darkrai said while they could do nothing but be dragged away.
"Amazing info you gave us, Greninja," Darkrai said.
"Master, there was something weird about that. Empoleon and Sceptile said that when they got there, the control panel was already unlocked, and it wasn't part of a trap of mine," Aegislash commented.
"That is strange," Darkrai replied.
"If you want, I will check it out. You two need to get ready for the final plan," Greninja said.
"That is a great idea. Go right ahead, Greninja. I will send you access to it," Darkrai said, to which Greninja immediately started heading towards the control room.
"Master, I still have a bad feeling about Greninja, like they are up to something," Aegislash said.
"You're letting your paranoia get the better of you. Greninja has proven to be a trustworthy ally. Now come on, I need your help with the final preparations," Darkrai said.
Greninja parted ways with Darkrai and Aegislash. They went to the control panel and quickly received full access from Darkrai. Everything had gone exactly as they planned for it to go. Greninja felt extremely proud of themselves.
Greninja untransformed, revealing herself to have been Zoroark the entire time. She had been spending all of this time slowly infiltrating the Brotherhood. Now she had full access to the control panel on the day of the ultimate plan of The Brotherhood.
"Everything went exactly as planned, and you were none the wiser, Darkrai," Zoroark says with a smile.