After liberating Mount Battle from Team Shadow, Wes and Rui have been on high alert, knowing Team Shadow will strike again.
Weeks have passed since the last Shadow Pokémon was reported. Wes and Rui knew Team Shadow weren't calling it quits at all.
But it wasn't long until Wes became well-known for foiling the Team Shadow operations.
The first place they're heading to is Pyrite Town.
The first person they see there is Cail.
"Oh, it's you again," Cail said.
"Cail, you know what's going on with Pyrite Town?" Wes asked.
"Granted that things have been pretty quiet around here ever since Miror B and his people were driven out by you," Cail said.
"Has there been any recent sightings of Shadow Pokémon lately?" Rui asked.
"No, not since your stunt on Mount Battle. But even Officer Johnson knows it'll be a matter of time until they make their next move," Cail said.
"At least we know things have been quiet," Wes said.
"Too quiet," Wes said. Rui looked right him. "They'll make their move again and we gotta be on top of them."
"You're right," Rui agreed.
Things were peaceful despite Miror B no longer running the operations, but it still has its reputation for being the home of thugs and lowlives. For one thing, Johnson was still incompetent as ever.
They went over to Duking's place to talk to him.
"Wes, Rui. I heard. Thank you. You did it again. But... We don't know why they would go after Mount Battle," Duking said.
"We know," Wes said.
"The reason they were even after Mount Battle is because they wanted to get their hands on the Time Flute," Rui said.
"Ah, so that's why. The Time Flute is connected to the Relic Stone in Agate. Both are very important," Duking said.
"We figured as much. Just as we figured that the Time Flute can only be played at the Relic Stone to call Celebi and purify the Shadow Pokémon," Wes said.
"But the problem is, we don't know how many Shadow Pokémon are left and who has one," Rui said.
"Yes, that is a problem. You better figure it out and fast before it gets even worse than it already is," Duking said.
"You can count on us, Duking," Rui said. Duking just smiled.
"I know I can," Duking said.
As they stepped out of the building, they spotted what looks like a Team Shadow peon lurking around.
"Wes, look!" Rui said.
"I see him," Wes said.
They chase after him. The peon ran toward the building Miror B once occupied.
"That's Miror B's old hideout," Rui said.
"He must be baiting us. I think I narrowed down one of two scenarios. He's either leading is to Miror B to have his payback against us, or he's some random Miror B groupie trying to get a piece of us," Wes said.
"Well, he made a mistake in challenging us," Rui said.
"That's saying it, Rui. Let's go," Wes said. Wes and Rui followed the Team Shadow peon to the building. They went up the stairs and out the door, knowing the only place to go was to the caves. They weren't disappointed when they him inside the cave. They've chased him throughout the cave right until they have him trapped in Miror B's lair. "You have nowhere else to run! You're trapped."
"You have me. You have me," the Team Shadow peon said, raising his hands up in surrender. Wes was caught off guard. He sensed there was something off about him. He summoned his Colosseum of Light and pointed it at him.
"Okay, you. Who are you really? You're not really with Team Shadow. You're just someone else, aren't you?" Wes asked. The Team Shadow peon just grinned and he lowered his hands.
"That is correct," the Team Shadow peon said as light flashed all around him and it's revealed to be DiZ.
"Who are you?" Rui asked.
"I have been called many names in my life, but you can refer to me as DiZ," DiZ said.
"DiZ? That's a name I'm not familiar with. Why did you drag us here?" Wes asked.
"Merely to talk," DiZ answered.
"Talk about what?" Rui asked. She then gasped. "Wait, are you with Team Shadow?"
"No. I am not an ally of your enemies," DiZ said.
"If you're not with Team Shadow, then what do you want with us?" Wes asked.
"What you need to know is that we have a common enemy," DiZ said.
"A common enemy?" Wes asked, raising a brow.
"Are you talking about Team Shadow and the Shadow Pokémon?" Rui asked.
"The enemy I am speaking of is far more powerful and more deadlier than Team Shadow. In fact, this enemy was the one who is truly behind the Shadow Pokémon's creation," DiZ said.
"What is that supposed to mean?" Wes asked.
"The enemy have been allowing Team Shadow into closing the doors to their hearts, thusly becoming creatures of darkness," DiZ said.
"So, Team Shadow's not the real threat like we thought?" Rui asked.
"No. They're merely pawns in their game," DiZ said.
"You obviously know who this enemy is, don't you? If you do, then just tell us. Don't beat around the bush," Wes said.
"The enemy goes by the name of Organization XIII. They are the ones who are behind this nefarious scheme," DiZ said.
"Organization XIII?" Rui asked.
"A group of 12 out of 13 individuals working towards a goal. One of those goals is to find their 13th and final member. And the other is to gather many hearts as possible. The Shadow Pokémon are one of those keys into meeting their goals," DiZ said.
"Why would these people need Shadow Pokémon for?" Rui asked.
"There is darkness in all hearts. When one feeds the darkness within their hearts through rage, hatred, or jealousy, then one would turn into a Heartless. Even Pokémon can turn into Heartless," DiZ said. Rui gasped in shock.
"You mean, those Heartless used to be people and Pokémon?" Rui asked.
"I am afraid so. However, the Organization has become aware of your accomplishments, which is the reason I am reaching out for you. But the choice will be yours. Will you continue to aid me in my campaign against the Organization or will you resign after the last of the Shadow Pokémon has been liberated from the Organization's control?" DiZ asked.
Wes and Rui looked at each other.
"Wes, what do you think?" Rui asked.
"I don't know if we should trust him. This guy is rather on the shady side. How do I know he's not with those Organization XIII guys he mentioned?" Wes asked, skeptical.
"But if they're the ones pulling Team Shadow's strings, then we gotta stop them," Rui said.
"We're getting in too deep. We already have our hands full dealing with Team Shadow and thr Heartless. But I can't argue that you're right. The Organization has to be stopped," Wes said.
"So, you're saying that we should help out?" Rui asked.
"For right now. I just have a hunch he knows more than he's letting on," Wes said. They turned to DiZ. "Alright, DiZ, we'll lend a hand however we can."
"You have made a wise choice," DiZ said. "The next part of your Shadow Pokémon crusade shall lead you to the Under."
"The Under?" Wes and Rui asked.
"And that is all I can tell you," DiZ said as he vanished.
"Hey, wait!" Wes called out. "He didn't even tell us how to get there."
"Maybe he plans for us to figure it out," Rui said.
"If he's trying to send us on a wild Zangoose chase, then I'm gonna break his nose the next time I see him," Wes said.
Over to the World That Never Was, Saïx came in through a corridor of darkness to make his report to Xemnas.
"Saïx, what have you discovered?" Xemnas asked.
"Lord Xemnas, I have completed my thorough investigation, and I found out that there are two individuals that were causing some damage for the Shadow Pokémon plan. And I found out that there are two people on the case. One is a girl who has the ability to see the black aura and no one else can," Saïx reported.
"And the second one?" Xemnas asked.
"From what I can gather, the other one is a boy, so he has a Snag Machine and he's using it to take the Shadow Pokémon from them. That's how he was able to do it. And just weeks ago, they came across something called the Time Flute and the Relic Stone. They were using it to purify the Shadow Pokémon from our control," Saïx said.
"Then the faces of our enemies have been revealed. Dealing with them has become our priority," Xemnas said.
"Yes, Lord Xemnas," Saïx said.