Previously on Pokémon: The Lost Child, Empoleon, Sceptile, and Aegislash made their way to the home of the gods, the spear pillar. Once they arrived, they found Deoxys locked in a battle with two other gods. The trio assisted, and with the help of them plus Victini, they were able to force the two to retreat. Now, however, the trio is demanding more answers for what is going on, and now Deoxys feels that he doesn't have a choice.

"Alright, I need to start from the beginning." Deoxys took a deep breath before continuing, "A long time ago, in the very distant past, the universe was a very different place than it is now. Everything was wild; there were no organized villages, and every single Pokémon was out for itself. The god of the Pokémon universe, Arceus, was still around."

"Wait, so we were right Arceus was indeed real," Sceptile said.

"Yeah, you were correct; he is very real indeed. Arceus was not the benevolent god that you might think that he was he was a power-hungry tyrant who treated the land he created as slaves. The rest of the gods had been treated just as terribly, as we didn't have the power to stand up to him individually."

(Flashback)

"Brothers, we can't let this continue; we have to take power back for ourselves; together, we will take this land and free the people," Deoxys said.

"Why should we let Arceus push us around like this? You are right," Raikou said.

"Alone, none of us can stand up to him, but together, we might have a chance," Darkrai said.

"Everyone who is with me, raise your hands," Deoxys said. Everyone nearly right away would raise their hands at the moment all of them knew that they were in this together it was time for the beginning of a revolution.

In the meantime, Arceus was watching over the world that he had created inside of the spear pillar. Arceus had done this kind of thing often, where he was thinking up some punishment that he could give the rest of the Pokémon. The rest of the gods, though, had come inside the spear pillar, ready to overthrow Arceus. Arceus had not noticed they had come in, but eventually, he heard someone behind him and turned out to see a massive crowd of the gods.

Arceus didn't know what was going on, but the sight of all the gods coming up to him like this was terrifying, as it could mean they wanted to do something bad to him.

"I order all of you to stand down," Arceus said.

"We refuse Arceus," Deoxys said.

"I command you all to step down this instant," Arceus said in an extremely aggressive and demanding tone that several of the gods were put off by.

"We are tired of being pushed around by you, Arceus; we are taking a stand; treat us better, or else you will have to face all of us," Zapdos said.

"You are all easily replaceable, and I do not care at all. The punishment for defying your god is death," Arceus said. Arceus then launched an extremely powerful blast at them, the move that Arceus liked to call his "Judgment." The gods knew this was likely going to happen and were able to react quickly enough to dodge out of the way. It was Arceus versus all 59 of the other gods. Arceus should have stood no chance, but his power far exceeded all of theirs, and they were genuinely unsure if they would be able to defeat him, but they had to try.

(Back to the present)

"I had no idea that Arceus was like that," Sceptile said.

"It honestly doesn't surprise me, I had a feeling that was the case as well," Aegislash said.

"Yeah, there was a reason we all hated him. Anyway, back to what I was talking about," Deoxys said.

(Flashback)

Arceus fired judgment after judgment at the gods, aiming for each of their deaths. The battle was catastrophic as the spear pillar was destroyed from all the carnage, and the battle spilled out into the main world where the gods would continue fighting Arceus.

Each god was firing off attacks at Arceus to weaken him, which Arceus was just shrugging off and taking no damage from. Around 5 of the gods had already been killed, and they had done no damage to Arceus at all. Deoxys knew that this was not working and knew they needed to think of a new strategy. Deoxys had a backup plan in case they weren't able to take Arceus down in a head-on-head battle.

"Everyone follow me to our base. We need to discuss a new strategy."

All of the gods stopped fighting Arceus and fled to the base. Arceus was mad that he wasn't able to finish them off and started yelling, "You can run, but you can't hide. I will find you all, and you will all face my judgement."

Each of the gods made it back to the base where their revolution had first been concocted. It was only temporary, as all of them knew it was only a matter of time before Arceus found this one and they were all in trouble.

"So Deoxys, this is not working, you better have something good."

"I understand the frustration. I do have another idea, but it is unfortunately very risky and might lead to a few of us dying. But at this point, it might be the only option that we have left."

"Tell us, Deoxys, it can't be any worse compared to what Arceus will do to us," Darkrai said.

"I have discovered the existence of other realities beyond our own, and if we create enough energy, we can use it to transport Arceus to another reality, one where he can't do anything and can never return. Think of it as some kind of interdimensional prison," Deoxys explained.

"Well, that sounds like the best option that we have," Zapdos said.

"I fear that you are probably correct," Deoxys said.

"So tell us the plan, Deoxys; we are willing to go along with this if you think this has a chance at working," Suicuine said.

Deoxys would tell the rest of the gods what his plan was, and eventually, all of them were ready to either take down Arceus or die trying.

All of the gods flew or walked up to Arceus as he was travelling across the world to look for them. Arceus didn't fully expect them to make a bold entrance instead of continuing to hide and asked, "So have you come to accept your fate?"

"Not quite, everyone now." On Deoxys's command, the rest of the gods all started pinning Arceus down, using all of the strength they had combined to hold him down. Arceus was struggling to get all of them off of him.

At the same time, Deoxys and another god named Mewtwo began their ultimate plan. Deoxys and Mewtwo would use their psychic powers to link themselves together and open a rift in space-time. Every second counted, so they had to get started as soon as possible.

"Are you ready?" Deoxys asked.

"It's now or never," Mewtwo responded.

Both of them began the process: they linked their minds together and started concentrating hard; they were able to focus enough to see into other realities and eventually managed to get into one where there was nothing but space. It was the perfect place to banish Arceus to, as there was no way that he could ever return.

Mewtwo and Deoxys opened up a tear in space-time right behind Arceus, then the rest of the gods began stage three of their plan. They used all the strength they could muster to push Arceus back far enough. Arceus tried to resist, but he wasn't fully able to push back all the power quickly enough. He was getting slowly sucked into the rift, and he knew it.

Arceus started screaming out, "This can't be!"

"Your reign of terror, Arceus, is about to end." Deoxys made one last push to send Arceus into the rift. However, in one last act of desperation, Arceus fired a judgment that hit the middle and, as a result, killed a few of the gods. Deoxys survived, but Mewtwo was not so lucky.

They were able to seal Arceus away, but the gods took the time to mourn their fallen brothers. However, it wasn't meant to last, as the vacuum of power had fallen and the rest of the gods were scrambling to take power. Darkrai was among them, and that is how he ended up creating the Brotherhood in his quest to assume power over the world.

(Flashback ends)

Deoxys finishes by saying, "Little did we know Arceus, even in his dimensional prison, was not completely powerless and was still able to influence things in our world."

The trio could only sit there in utter disbelief at what they had just learned. Empoleon and Sceptile were stunned. Aegislash was surprised, but he hadn't discounted this possibility, so it wasn't quite as surprising for him, though still unexpected.

"Once Arceus returns," Empoleon said, then Deoxys said, "Yes, it will be the end of all of us."

"We have to stop him then, maybe if we work together, we can do it before it is too late," Sceptile suggested.

"I worry that we may already be too late, the fighting between the gods has damaged the stability of space and time. There is a plot unfolding that I suspect Arceus has been orchestrating from behind the scenes all this time, he will find a way to release himself," Deoxys said.

"We can't give up hope," Aegislash said. Hearing the words coming from him specifically was very shocking to both Empoleon and Sceptile.

"You mean that?" Empoleon asked.

"I am not a great Pokémon, I will admit, but I want to keep my own life; if there is a way we can stop Arceus, we can take it."

"There is one thing we might be able to do," Deoxys said.

"Why don't you tell us?" Sceptile suggested.

"It is going to be rough, but it is our only chance," Deoxys said.