Previously, in Pokémon: The Lost Child, Empoleon and Sceptile were lost in the woods before they were helped by a Victreebel living in the woods. They would discover, however, that Victreebel had been killing Pokémon to steal their supplies. Victreebel attempted to kill both of them, but they were able to escape and kill Victreebel in return. The two were now able to leave the woods, but little did either of them know that there was a new foe hunting them down who had now located his prey.
"We haven't seen any kind of village for a long time," Sceptile was commenting.
"There has got to be one coming eventually, though it is weird just how quiet it is around here," Empoleon responded.
"We haven't had any sort of proper battle since the encounter with Aegislash," Sceptile said.
"I guess we should consider ourselves fortunate that there is nothing we need to worry about right now," Empoleon said, while at the same time, Dark Empoleon was watching, waiting for what could be the perfect opportunity to strike. At the same time, Darkrai was hearing about everything that was going on and keeping track.
"Dark Empoleon has found the two and soon they will be out of my way, permanently," Darkrai said. Dark Empoleon, in response, simply said nothing. He just nodded. He knew what his job was and was ready to do so without any hesitation.
"Hey, Sceptile! I have been wondering something," Empoleon commented.
"What is it?"
"Is there any Pokémon like me out there? Like another Empoleon, we have seen multiples of the same Pokémon before."
"It's certainly possible each species of Pokémon has many members, with some exceptions like the god Pokémon."
"I do hope I get to see another Empoleon at some point. That also does bring up a question I have had: where does this god Pokémon come from?" Empoleon asked.
"I honestly have no idea. It is quite weird," Sceptile responded.
"That is unfortunate."
"This world is still full of mystery. We barely know anything about it, honestly, maybe it is better that we know so little. Who knows if we would be able to handle the knowledge," Sceptile said.
While Sceptile was talking, he was starting to hear some noises, rustling grass, footsteps, and grunts that were getting louder as time was passing. "Empoleon something is coming. Watch out!"
"I can hear that as well." Empoleon and Sceptile braced themselves, expecting the worst but hoping for the best. They both knew the Brotherhood was going to start chasing after them, and they were ready for whatever they could throw at it. They were expecting to see Aegislash again, but it quickly became apparent something else was up. This force approaching them was less careful. He was rushing towards them but in a way that they couldn't see.
"What is going on? I can't see anything," Empoleon commented.
"I can't either but I can still hear the noises. This doesn't feel like Aegislash, whatever it is it's." While Sceptile was saying, he was interrupted by a sudden strike from the back. It was some sort of sharp claw. The Sceptile went flying forward away from Empoleon.
"What in Arceus' sake?" Empoleon, after hearing what happened, turned around and saw another Empoleon, but completely black, standing right behind him. The Dark Empoleon hit Empoleon with his claw, sending him flying back, but he was able to land on the ground to see what was going on. Empoleon tried to shoot a bubble beam at Dark Empoleon, but Dark Empoleon teleported and struck Empoleon from behind and launched him towards where Sceptile was.
"What is this thing?" Empoleon asked.
"It's another Empoleon one just like you, but something is very wrong about this one," Sceptile said.
"When I said I wanted to meet another Empoleon, this is not what I had in mind."
"Maybe you should have chosen your words a bit more carefully," Sceptile responded.
"Do you think that The Brotherhood is behind this?" Empoleon wondered.
"I am not sure, but it seems very likely," Sceptile responded.
Dark Empoleon teleported right back up to them with Empoleon trying to strike Dark Empoleon with his claws, but Dark Empoleon continued to dodge out of the way of every attack.
"What kind of speed is this?" Sceptile asks as he is changing towards Dark Empoleon, but he effortlessly dodges out of the way and strikes Sceptile with another darkness-embedded claw.
Using the distraction, Empoleon was able to get a single hit on Dark Empoleon with his claw, but it barely seemed to affect him at all. Dark Empoleon instantly struck back with some super powerful water and darkness mixed canon of water, which knocked Empoleon back.
"How are we supposed to beat this thing?" Empoleon asked.
"I don't know if we can; our only option seems to be to run at this point," Sceptile said.
"I don't like that, but I have to admit that might be the only choice we have at this point. We may not have a choice."
Empoleon took the suggestion and, along with Sceptile, the two ran away as fast as they could. However, it was proving to be difficult to get out of Dark Empoleon's sight as he was extremely fast and able to teleport at will. Empoleon and Sceptile eventually spotted a cave and knew that could be a good place for them to hide for at least a bit until they thought of a new strategy.
They were able to duck out of sight of Dark Empoleon and hide inside the cave with Dark Empoleon looking for where they hid.
"What is this thing?" Empoleon wondered.
"I don't understand the power, the speed, where is this thing coming from," Sceptile commented.
"It is clear we won't be able to take this thing on directly. We need a different plan," Empoleon suggested.
"I don't know if we have the power to take this thing down. However, I do have an idea. What if we used its power against it," Sceptile thought.
"That could work, but we need to be very careful. A single mistake could screw everything up," Empoleon said.
"Let's think it can teleport, it can induce its claws with darkness and it has some water moves," Sceptile said.
"If it can teleport, we need something that can prevent it from teleporting, so it can't teleport for some time," Empoleon said.
"I think I have an idea," Sceptile responded.
Empoleon and Sceptile come out of the cave. Dark Empoleon is still looking for the two, and Empolen and Sceptile are all too happy to help. They start yelling out, "Over here if you want to fight," as loudly as they can. Dark Empoleon notices the noise nearly instantly and rushes over to where it is coming from.
When Dark Empoleon arrives, it is right next to a tree with no Empoleon or Sceptile in sight. The tree he is standing next to falls down, but Dark Empoleon teleports out of the way and goes to where the tree was chopped down but sees that there is nobody there. Dark Empoleon is instantly hit by a trapdoor as he falls to the ground, where he finds himself in some underground tunnels. Dark Empoleon was initially going to teleport out, but he heard Sceptile saying, "He's never going to find me," all over the place.
Dark Empoleon rushes forward and sees Sceptile very quickly. Sceptile starts running away, hiding behind multiple pillars, which Dark Empoleon destroys very quickly with his various attacks. However, little did Dark Empoleon realize that each pillar he was destroying was causing the support structure to become weaker. After destroying nearly every pillar, the cave would collapse in on itself, trapping Dark Empoleon inside and knocking him unconscious. Sceptile was able to escape as he knew all the secret passages.
"How did the plan go, Sceptile?" Empoleon asked.
"It went perfectly. He is trapped down there. Nice work knocking down the tree with your water. I knew that he would never see that coming," Sceptile responded.
"We should get out of here as quickly as we can before that thing wakes up if he does," Empoleon commented.
"I couldn't agree more." Right after, Empoleon and Sceptile started running away as quickly and as far away as they could while Dark Empoleon was still unconscious on the ground.
Meanwhile, Darkrai had quickly been made aware of what was going on and how his creation managed to somehow get knocked unconscious. After a few hours of travelling, he went over to where he had been buried and shattered all the rocks he was buried under.
"What is going on?" the Dark Empoleon said, finally speaking for the first time.
"It looks like my brainwashing is wearing off. It's time for me to fix that." Darkrai clenched his arm, releasing a nightmare into Dark Empoleon's mind, causing Dark Empoleon to scream out in agony while Darkrai was brainwashing him again.