Previously on Pokémon: The Lost Child, Empoleon and Sceptile found Aegislash sitting in a garden, who wanted to tell them some very important information. As Aegislash was talking to them, the three of them were attacked by a Giratina, which they were barely able to fend off. Empoleon and Sceptile formed a reluctant alliance with Aegislash to find and combat the rise of a potential new threat, Arceus.
"Where are you taking us, Aegislash?" Empoleon asked.
"Darkrai has mentioned this place before, the tower of the gods; it is called Spear Pillar," Aegislash said.
"I have never heard of that place before," Sceptile said.
"It is very hidden from most of the world, and only a very select number of Pokémon know about its existence," Aegislash said.
"I guess we are lucky that you know about it," Empoleon said.
The three continue going up the incredibly dangerous mountain, surviving through the harsh cold to eventually reach the gates of the spear pillar. The three started at the massive gate that was the last obstacle to the spear pillar.
"I have always wondered what this place looks like, it is time," Aegislash said.
Aegislash pushed open the gate to the spear pillar. A flashing light briefly blinded them, but once they were able to see what was happening, it was nothing like the paradise they all assumed it would be. The spear pillar was in flames; everything was on fire, major parts of the place had been destroyed, and multiple Pokémon were fighting each other.
The three were shocked to see this and could only wonder what happened to cause all of this.
Inside the spear pillar, Deoxys was fighting with Palkia at the moment. The trio did not know why they were fighting, but they could see what was going on.
Palkia keeps trying to blast Deoxys with various water moves, but Deoxys uses his speed form to dodge out of the way. Once he gets close to Palkia, Deoxys shifts into his normal form, and the two clash, each trying to hold the other back.
"Palkia, we shouldn't be fighting each other; if we work together, we can stop him," Deoxys said.
"I will overthrow him and become the new god of this world; don't get in my way," Palkia said.
"Don't make the same mistake he made years ago, we have to work together if we want to stop him," Deoxys pleaded.
Palkia, however, didn't listen and kept trying to swipe Deoxys. Deoxys dodged out of the way and launched a psycho boost at him in retaliation. Deoxys then charged up to Palkia to continue the fight.
Empoleon, Sceptile, and Aegislash witnessed that entire series of events and could only stand there in utter confusion and disbelief at what they had just witnessed.
Another Pokémon fell from afar onto the ground, severely injured. They fell right next to the trio, so Empoleon went up to check if they were okay. The Pokémon that fell on the ground was Jirachi, who had been in a fight and had been injured heavily,
"Are you okay?" Empoleon asked.
"Who are you?" Jirachi asked as it opened its eyes very slowly.
"What is going on here? Why is all this fighting happening? We don't understand?" Empoleon asked.
"The gods are, in a way, in a war for control, and the father is about to be released," Jirachi passes out right there Empoleon initially thinks it died, so he checks, but luckily realizes it is alive.
"Father, you don't think that means?" Sceptile said he was waiting for Aegislash to respond. To which he responds with, "Unfortunately, I think it is, my theories are true, Arceus is the root of whatever is going on, and if what Jirachi said is true, we don't have much time left."
"We need to get some information from Deoxys, but he won't be able to tell us anything unless he defeats that Palkia," Empoleon said.
"Well, I guess that we will need to help then. We have taken down a god together before, so maybe we can do it this time as well," Sceptile said.
At the same time, Deoxys and Palkia continued fighting, but soon they were not alone. Dialga joined and started using the roar of time to try and catch Deoxys. Dialga and Palkia were hardly friends. The two were also trying to hit each other with their attacks while Deoxys was getting in between them, trying to stop them from fighting.
"If you two won't stop fighting I will need to force you two to stop, you hear me?" Deoxys said.
Dialga and Palkia didn't listen though and continued attacking each other anyway. Deoxys launched some psycho boosts at them to try and get them to stop fighting each other, but they were making very little progress.
The trio ran up to the general location where the three were fighting in, and Sceptile yelled out, "Deoxys!"
"What, what are you three doing here?" Deoxys said.
"We are here to help; we know what is happening, and we need to help stop this," Empoleon said.
"You shouldn't be here. Get out of here. You don't stand a chance against anyone here." Deoxys, while he was talking, got blasted with another roar of time and was able to quickly block it by switching into his defense form.
"We can help. We were able to defeat Giratina by working together," Empoleon said.
"Wait what? How is that even possible? You should not have been able to do that," Deoxys said.
As Palkia was attempting to fire a spacial rend at Deoxys, Aegislash saw it and launched a shadow ball up in the air. Hitting the spacial rend and preventing it from hitting Deoxys.
"Hmm, that is impressive, I have to admit," Deoxys said.
As Dialga was attempting to attack Deoxys with his roar of time, another god Pokémon showed up. This one was defending Dexoys instead of attacking. This Pokémon had a V on its head and was able to light it on fire, which it then used to destroy the roar of time.
"There you are, Victini," Deoxys said.
"I am always fashionably late, as they say," Victini responded. A comment that everyone else cringed at.
"Let the big boys do the talking, Victini," Palkia said.
"Hmm, I am going to go with a no on that one." They charged toward Palkia at breakneck speed after Victini said that, covering themselves in a massive electric orb and charging straight at Palkia with it. Palkia did not see it coming and wasn't able to block it in time, so he took the hit and was sent flying back.
"What the?"
"A little bit of a new trick that I learned, and you are going to love it," Victini said while laughing slightly under her breath, something that Palkia found incredibly irritating.
"Don't get too cocky, Victini," Deoxys said.
Aegislash floated up into the air right next to Victini and Deoxys as they got ready for battle. Empoleon and Sceptile aren't able to float, so they were concerned about how they were going to fight, as Sceptile vocalized, "I don't know how we are going to help like this."
"Don't worry, I have you two covered." Victini cast some kind of luck charm on them, which instantly floated Empoleon and Sceptile up into the air. Victini was quick to inform them though, "It isn't permanent though, so try to make use of it."
"If these are the best you have, Deoxys, this is going to be easier than we thought," Palkia arrogantly said.
The battle had now fully begun. It was to be an intense battle, a battle of the gods, with Empoleon, Sceptile, and Aegislash tagging along. Empoleon and Sceptile went after Dialga right away. Sceptile launched a dragon pulse and Dialga to distract him while Empoleon flew forward and clashed Dialga with his claw. Dialga, however, was able to block it and counter. However, Victini used this chance to hit Dialga with her v-create move which hit for a lot of damage.
"That thing is way more powerful than I expected," Dialga said.
"You have only seen the half of it," Victini cockily said.
Victini then starts flying around Dialga, pummeling him with v-crates, fusion bolts, and fusion flares, all of which are hitting Dialga for decent damage.
At the same time, Aegislash and Deoxys are taking on Palkia. Palkia is trying to hit Deoxys with a hydro pump, which Deoxys keeps dodging out of the way with his speed form. Aegislash fires a Shadow Ball at Palkia, which he is able to use his spacial rend to destroy before it hits him. Palkia is already starting to struggle with two of them on him at once, including another fellow god.
"This approach isn't working, we both attack him at once," Deoxys said to Aegislash, making sure to say it out of Palkia's hearing so he doesn't see it coming.
"Got it. I go from the right. You go from the left."
Both Deoxys and Aegislash went with that plan. Deoxys teleported next to Palkia and charged forever to hit him with a massive punch. At the same time, Deoxys flew from the other side next to Palkia and tried to slash him with his sword. Palkia was trying to block both attacks with his arms, but it was taking all his strength to do so.
Palkia's defence was broken through, and both hit him at the same time for a massive blow.
Dialga and Palkia were outnumbered and outmatched, and both knew they had to retreat to fight another day. They both very quickly fled the spear pillar, leaving just the five.
"Man, that was a close one. Thanks for the help everyone," Deoxys said.
"You probably couldn't have done it without us," Victini said while laughing slightly.
"I still need to know you three, what are you doing up here?"
"We were almost killed when we were attacked by Giratina after Aegislash told us about Arceus. We came because we demand answers, Deoxys," Sceptile said.
Deoxys' heart briefly sank when he heard that, but now he knew what he had to do, "I wish that it hadn't come to this. I guess there is no point in keeping the truth from you guys now. To get an idea, we need to start from the very beginning"