Previously on Pokémon: The Lost Child, Empoleon and Sceptile, along with Zoroark, were successfully able to take down The Brotherhood. It was not without its challenges, but it seemed that all that they had been working for had finally been completed. However, suddenly, a massive explosion went off inside the base, destroying it and seemingly everyone inside. The three heroes were only barely able to escape thanks to some assistance from Deoxys, but they were all left dumbfounded and perplexed at all of this.
Empoleon, Sceptile, and Zoroark, from the distance, were staring down as the base slowly turned into nothing but dust. There was seemingly nothing left, it was all gone.
Zoroark had an immense wave of satisfaction; it felt like her life's work was finally complete. Sceptile and Empoleon were both pleased, but not as much as Zoroark; it all seemed so simple, and they couldn't figure out what was causing the explosion. The explosion, this one thing that came at the very end, made so little sense.
"I did it, I finally did it," Zoroark said before taking a slight breath and adding on, "The age of The Brotherhood is over."
"So what now, Zoroark?" Sceptile wondered.
"Honestly, I had never thought about that; my whole life had revolved around taking The Brotherhood down, and now that they are gone, I don't know what else to do."
"I like to think of it this way, this is the beginning of a new chapter in our lives. Now that the Brotherhood is gone, it is your chance to do something for yourself," Empoleon said to Zoroark.
"I think I understand that, thanks, Empoleon. It is time for me to make a difference." Zoroark tried to walk away, but before she could, she turned around to say one last thing to Empoleon and Sceptile, "Thanks for all of the help; I couldn't have done it without you."
"I am still not happy over the stunt you pulled that nearly got us killed," Sceptile commented.
"I do understand that, and I hope that you will come to understand eventually; for now, though, it is time that we part ways," Zoroark responded.
Empoleon and Sceptile waved Zoroark goodbye as she walked into the distance to begin a new chapter in her life. Sceptile and Empoleon were there, just the two of them, looking at the destroyed base of the Brotherhood. They couldn't stop thinking about how weird all of this was, and they were both about to make their intentions clear.
Sceptile walks up to the base of the Brotherhood, which is now nothing but dust, he comments, "I don't understand how this happened."
"I don't understand it either, I fear that we may never know," Empoleon responded.
"Yeah, you're probably right."
"The bigger thing that I am wondering is: of all the Pokémon inside, did any of them survive," Empoleon wondered.
"It doesn't look like there were any survivors; everything is gone, all of it turned to dust. I doubt anyone could have survived that, not even someone like Aegislash," Sceptile responded.
"Well, we did manage to survive," Empoleon pointed out.
"That is true, though we only survived due to being teleported out at the last second. We would have died inside there if it wasn't for that," Sceptile mentioned.
"Yeah, that's right, the teleportation," Empoleon said after realizing that.
"I suspect that Deoxys had something to do with that. Remember the last time we talked to him and what he said?" Sceptile said.
"Yeah, I remember something about how the Brotherhood is a piece of a much larger puzzle."
While Empoleon was answering, a voice in the distance said, "You got that right, Empoleon." Empoleon and Sceptile looked over to see that it was none other than Deoxys himself.
"Speak of the devil," Sceptile said.
"Yes, it was me that saved you from the base of The Brotherhood," Deoxys answered.
"Thanks for that, Deoxys," Empoleon responded.
"I did owe you one, you did save me not too long ago as well," Deoxys clarified.
"I thank you for that as well, Deoxys. "But I need to know; we took down The Brotherhood; now tell us what's next; you alluded to some kind of greater threat," Sceptile inquired.
Deoxys reacted to that question with a sad look. It was like Deoxys didn't want to be asked that and knew that the two would be disappointed with the answer they were about to be given.
"Tell us, Deoxys," Sceptile demanded.
"Look, Empoleon, Sceptile; there is nothing more that I would like to do. One day you will understand the most I can tell you, which is that there is a massive threat coming from something far beyond what you have faced before. I can't tell you too much or else they won't be able to be stopped; in fact, I am afraid I may have already said too much."
"Stop with these games, Deoxys; tell us what we need to know," Sceptile said, getting angrier and angrier at Deoxys' constant vague statements.
"Sceptile, please calm down. We have to understand there are things beyond us," Empoleon said.
"I understand why you are mad, Sceptile, but listen to your friend," Deoxys said.
Sceptile calms down slightly before continuing, "Alright if you won't give us any details, tell us what we need to do. Can you at least do that?"
"Okay, what you need to do is train, get stronger and stronger to prepare for what is coming, and never think you are strong enough, you may never be, but you have to try," Deoxys said.
"There we go, Sceptile, we've got something to work with," Empoleon said.
"I am grateful for that much, but I still want to know more," Sceptile said.
"I fully understand that, and hopefully, in time, everything will be made clear to you." After Deoxys had finished, he started flying off into the distance. Empoleon and Sceptile were left there to continue pondering about what Deoxys told them and what it means for their future.
Empoleon goes back to the ruins of the base and keeps staring at it. Sceptile goes back up next to him and asks, "What is the matter."
"Maybe Deoxys is right maybe there is some bigger threat on the horizon, and they were the ones responsible for destroying this place," Empoleon answered.
"I suppose that is possible, but I am not sure if we will ever be able to figure it out," Sceptile responded.
"There is something else, remember the Slowking that we encountered that gave us a reading of sorts," Empoleon commented.
"Man, I'd almost forgotten about that; what did he say again?" Sceptile asked.
"Remember what he said about how I am the key and I need to find Arceus or something along those lines?" Empoleon replied.
"Yeah, that is right. Arceus, that name keeps coming up. Do you think that whatever they or it is could be connected to this?" Sceptile wondered.
"That is certainly possible. It begs the question though: how is he connected?" Empoleon wondered.
"That is a very good question; I have no idea how we would begin knowing that though," Sceptile said.
"Deoxys is a god Pokémon; perhaps he knows something," Empoleon suggested.
"It's very possible that he does, but considering what he is like, it seems rather unlikely that he will tell us anything," Sceptile pointed out.
"That is a good point," Empoleon said.
Empoleon and Sceptile were stuck at a dead end, with no good answers to any of their many questions and no idea of where to go next. After a bit of time, one idea came to Sceptile's mind.
"Hey, Empoleon remembers that village that The Brotherhood controlled; perhaps they know something that can help us," Sceptile suggested.
"That is a good thought; if nothing else, it's at least worth a try," Empoleon responded.
Following that, the two set out for the village. However, both of them had no idea that very dark prospects were beginning to form. The gang of Patrats that Empoleon and Sceptile defeated when they began their journey months ago were far away from where Empoleon and Sceptile are now.
Every single member of the Patriot gang is lying dead on the ground. All except one, that is. Watchog is crying over the bodies of his fallen friends, having no idea how this could have happened; he considered them family, and they all just died like that.
Watchog is spoken to by some sort of mysterious voice that says, "Listen, my child."
Watchog is spooked and shouts out, "Who's there? Show yourself."
"You cannot see me, but I assure you that I am very real," the voice said.
"I don't understand," Watchog said.
"You have suffered a terrible loss, and I am here to help you bring the Pokémon that did this to you, to justice," the voice said.
"Who did it?" Watchog asked.
"It is two Pokémon you are well familiar with, the Piplup and Treecko you encountered all those months ago, they did this to your gang. They have now evolved into Empoleon and Sceptile," the voice said.
"They will pay for this, I swear it on my life!" Watchog said.