After defeating Wes's former boss, Gonzap and turning down the offer to rejoin Team Shadow, Wes and Rui arrived to the colosseum at the top of the tower. They looked around and saw a roaring crowd. Nascour himself is approaching the couple and he evilly smiled.

"I'm glad you could finally make it all the way up here, Wes. I was almost beginning to think Gonzap had defeated you before you could get here," Nascour said.

"I'm glad to know you're not disappointed, Nascour. The time has come to end this," Wes said.

"How right you are, Wes. The time has come for you to pay off some debts. We'll have you battle as payment towards the huge losses you inflicted on us. I would have offered you a position into Team Shadow, but after all of the humiliation my people has endured because of you, I'm not that bighearted," Nascour said.

"Even if you were, I wouldn't be caught dead in your little club!" Wes said.

"I would feel insulted if you would be. I will destroy you in battle right now. You will know the humiliation of total domination before this crowd!" Nascour said as he took out two of his Pokéballs and threw them. "Dusknoir, Gallade! Go!" His Pokéballs opened and a Dusknoir and a Gallade emerged from inside to battle. Wes took out two of his Pokéballs and threw them.

"Espeon and Umbreon! Go!" Wes called out. Both of his Pokémon emerged from inside.

"Gallade! Thunderbolt on Umbreon! Dusknoir! Shadow Ball on Espeon!" Nascour ordered. Gallade fired a Thunderbolt at Umbreon as Dusknoir fired a Shadow Ball at Espeon.

"Espeon! Use Psychic on that Thunderbolt!" Wes ordered. Espeon does what he did with Sludge Wave. Shadow Ball explodes upon contact. "Use Dark Pulse on Dusknoir!" Umbreon fired Dark Pulse, hitting Dusknoir. "Use Psybeam on Gallade!" Espeon fired Psybeam, hitting Gallade.

"Dusknoir! Use Shadow Punch on Espeon!" Nascour ordered. Dusknoir lands a Shadow Punch onto Espeon. "Gallade! Use Psycho Cut on Espeon!" Gallade unleashed a psychic blade at Espeon.

"Umbreon! Protect Espeon!" Wes called out. Umbreon took the hit, but comes out okay, due to his immunity against Psychic-type attacks. "Psybeam and Dark Pulse!" Both Eeveelutions fired Psybeam and Dark Pulse, hitting the both of them. Dusknoir and Gallade had been knocked out, so Nascour called them both back and he took out two more Pokéballs and threw them.

"Blaziken, Xatu! Go!" Nascour called out. Both Pokémon emerged from inside. "Blaziken! Use Blaze Kick on Umbreon! Xatu! Drill Peck on Espeon!" Blaziken came at Umbreon with a Blaze Kick while Xatu does a Drill Peck and heads for Espeon.

"Umbreon! Dark Pulse on Xatu! Psybeam on Blaziken!" Wes ordered. Umbreon fired a Dark Pulse at Xatu, hitting it as Blaziken was struck hard with Psybeam.

"Blaziken! Use Aura Sphere on Umbreon!" Nascour ordered. Blaziken forms an Aura Sphere and sends it at Umbreon.

"Send it back with Psychic!" Wes ordered. Espeon uses Psychic to deflect Aura Sphere and sends it back with Psychic. Blaziken braced itself, but the Blaze Pokémon had taken some heavy damage and fell to the ground, beaten. He called Blaziken back and took out another Pokéball and threw it.

"Walrein! Go!" His Pokéball opened and a Walrein emerged from inside.

"Xatu! Use Dazzling Gleam on Umbreon!" Nascour ordered. Xatu hurls Dazzling Gleam at Umbreon.

"Dodge and use Feint Attack!" Wes ordered. Umbreon disappeared as Dazzling Gleam misses its mark. Umbreon reappeared and land a hit onto Xatu, knocking it out. Nascour called back his Xatu.

"I will admit, I underestimated you, Wes. You are even more powerful than I thought you were. I can see why my admins have lost to you, but you will not find me to be an easy opponent for you to defeat! And I have just the Pokémon to use against you! Go! Metagross!" He threw his Pokéball and a Metagross emerged from inside. Rui looked directly at Metagross.

"Wes, the Shadow Pokémon is that Metagross," Rui said.

"Gotcha," Wes said.

"Metagross! Use Shadow Shadow Storm!" Nascour ordered. Metagross unleashed Shadow Storm and sends it right at Espeon and Umbreon. Both Pokémon have taken some heavy damage from the attack. "Shadow Break!" Metagross charges at the both of them.

"Dodge it!" Wes called out. Espeon and Umbreon dodged Metagross's Shadow Break.

"Walrein! Ice Beam!" Nascour ordered. Walrein fired Ice Beam at Espeon and Umbreon.

"Psychic!" Wes ordered. Espeon uses Psychic to send Ice Beam straight up into the air. "Use Psybeam on Walrein!" Espeon fired Psybeam, hitting Walrein, confusing it.

"Metagross! Shadow Break on Umbreon!" Nascour ordered. Metagross rushed at Umbreon and deals heavy damage.

"Espeon! Psybeam! Umbreon! Dark Pulse!" Espeon and Umbreon fired a Psybeam and Dark Pulse combo, hitting Walrein, knocking it out. Nascour called his Walrein back, leaving Metagross as the only opponent.

"Shadow Storm!" Nascour ordered. Metagross unleashed Shadow Storm right at Espeon and Umbreon.

"Try to dodge it!" Wes called out. Espeon and Umbreon ran to dodge Metagross's Shadow Storm. "Psybeam and Dark Pulse!" Espeon and Umbreon combined their attacks once again and struck Metagross on the mark.

"Shadow Break!" Nascour ordered. Metagross lands a Shadow Break on the both of them.

"Feint Attack!" Wes ordered. Umbreon vanished and darts at Metagross, dealing some heavy damage. Wes took out an Ultra Ball and converted it into a Snag Ball. He threw the Ultra Ball, making it flow inside. The Ultra Ball wobbles around very violently until stars swirls around the Ultra Ball to confirm the catch.

"N-no! There's no... This can't be happening!" Nascour exclaimed. He grits his teeth. "Not only you have defeated me, but you snagged my Shadow Pokémon from me. No matter, because I will destroy you and-"

"Enough! Don't embarrass yourself, Nascour!" A familiar voice said.

"Sorry, sir. I beg your pardon," Nascour apologized.

"Nascour is apologizing?" Rui asked.

"To someone with a familiar voice," Wes said. The elevator came up and Es Cade stepped out.

"Wait, Mr. Mayor? What are you doing here?" Rui asked.

"My, my, my. I have seen such a more impressive battle in all my years. I never expected you to make it this far. You kinda took me by surprised to see me here of all places," Es Cade said.

"Why are you even here?" Wes asked.

"Ah, right to the point, I see. Perhaps I shall indulge you with an answer. Publicly, I am the affable mayor of Phenac City, but behind closed doors, I am Evice, the head of the criminal syndicate Team Shadow," Es Carde said, revealing his true colors to the couple. He laughed evilly. "Surprised?"

"But I don't understand. You were so kind when we first met! You're the real head of Team Shadow?" Rui asked.

"Indeed I am. You see, as mayor I was granted access to the city's assets, along with the Phenac Colosseum. Team Shadow provided Gonzap and his Team Snatch the Snag Machine to snag Pokémon who were the most appropriate candidates. Therefore, I allowed Team Shadow and Team Snatch to do as they pleased while I ran Phenac City, without any suspicions, but the only thing I failed to plan for is the two of you. I never would have imagined you would come and meddle in my affairs. If I knew this would happen, I never would have placed Nascour in charge of the Shadow Pokémon project," Evice said.

"That explains a whole lot," Wes said.

"But why?" Rui asked.

"Because with an army of Shadow Pokémon, I would overthrow all of the regions and rule the world, unopposed. But the only thing standing in my way for my ultimate goal is you two! I'll destroy you with the power of the ultimate Shadow Pokémon and begin anew! And this time, you won't be around to interfere!" Evice said. He took out two Pokéballs and threw them both. "Slowking, Scizor! Go!" Both Scizor and Slowking came out to battle.

"Espeon, Umbreon, you still good to battle?" Wes asked. Espeon and Umbreon nodded. "Go!"

"Slowking! Shadow Ball! Scizor! Silver Wind!" Evice ordered. Slowking fired a Shadow Ball while Scizor sends out Silver Wind. They managed to dodge their attacks.

"Umbreon! Dark Pulse on Slowking!" Umbreon fired a Dark Pulse on Slowking.

"Metal Claw!" Evice ordered. Scizor flew at Umbreon with Metal Claw.

"Use Feint Attack!" Wes ordered. Umbreon vanished and reappeared. Umbreon darts at Scizor, dealing some damage. "Dark Pulse, but aim it at Slowking!" Umbreon fired a Dark Pulse, hitting Slowking on the mark. Slowking was beaten. Evice called back Slowking and he took out another Pokéball and threw it.

"Machamp! Go forth!" Evice called out. His Machamp emerged from inside. "Cross Chop!" Machamp came at Umbreon with its four arms.

"Espeon! Use Psychic on Machamp!" Wes ordered. Espeon uses Psychic on Machamp and sent the Superpower Pokémon right on top of Scizor. The force of the landing was enough to knock Scizor out. He called back Scizor as he growled in anger.

"You insolent little-" Evice growled, taking out another Pokéball and threw it. "Salamence! Go forth!" His Pokéball opened and Salamence roared upon entry. "Dragon Dance and then Aerial Ace!" Salamence does a little dance, building up both attack power and speed. Salamence then dashed at Espeon and Umbreon, dealing some heavy damage. "Excellent! Machamp! Bulk Up and then, Cross Chop!" Machaml flexed its muscles and then came at Umbreon with another Cross Chop.

"Espeon! Psychic on Machamp!" Wes ordered. Espeon uses Psychic on Machamp, pushing it back. "Psybeam!" Espeon fired Psybeam, hitting Machamp, resulting in a knockout. Evice called back his Machamp and he took out another Pokéball and threw it.

"Slaking! Go!" Evice roared. His Pokéball opened and Slaking came out, pouding its chest upon entry. "Crush Claw!" Slaking charges at Espeon with Crush Claw.

"Psychic!" Wes ordered. Espeon gave Slaking a toss with Psychic.

"Salamence! Double-Edge!" Evice ordered. Salamence flew at Espeon with Double-Edge and deals some damage on Espeon.

"Recover!" Wes ordered. Espeon began to heal himself of his injuries.

"Salamence! Dragon Claw! Slaking! Crush Claw!" Evice ordered. Salamence and Slaking came at Espeon and Umbreon with Dragon Claw and Crush Claw.

"Psybeam and Dark Pulse!" Wes ordered. Espeon and Umbreon fired Psybeam and Dark Pulse, hitting the both of them. Both Salamence and Slaking were both knocked out. Evice called back Salamence and Slaking.

"I must admit, I underestimated you. I heard you were powerful, but you have power than I thought you did. But not even that will save you from the wrath of the ultimate Shadow Pokémon," Evice said, taking out his sixth and final Pokéball.

"I had a feeling Metagross wasn't the ultimate one. I thought Nascour was gonna let it out from the floor until you came. It all makes sense that you would have the ultimate Shadow Pokémon under your belt," Wes said.

"Smart boy. As my revenge, you will feel the wrath of the ultimate Shadow Pokémon! And that would be..." Evice paused as he threw it. "...Tyranitar!" His Pokéball opened and a Tyranitar emerged from inside. Rui saw the black aura from Tyranitar.

"The ultimate Shadow Pokémon is Tyranitar?" Rui asked.

"That's right. It was thanks to the genius of Ein that made this possible for me. Tyranitar is even more powerful than the Shadow Pokémon you previously encountered. But enough talk. I'll show you how it's powerful! Shadow Chill!" Tyranitar unleashed Shadow Chill and sends it at Espeon and Umbreon.

"Dodge it!" Wes called out. Espeon and Umbreon dodged Tyranitar's Shadow Chill.

"Shadow Bolt!" Evice ordered. Tyranitar unleashed Shadow Bolt and sends it at Espeon and Umbreon, so they dodged again. Evice laughed evilly. "Shadow Fire!" Tyranitar unleashed Shadow Fire, so Espeon and Umbreon dodged it again. "Shadow Break!" Tyranitar charges at Espeon and Umbreon. Evice laughed. "My Tyranitar's power is incredible! And I too feel powerful! With Tyranitar as my enforcer, the world will be all mine!" Evice laughed louder than he had before.

"You think your Shadow Pokémon is all that? Well, it's not! It's all about the bonds you share with your Pokémon!" Wes argued.

"What are you babbling about?" Evice asked, feeling irritated.

"It's the connections that humans shares with Pokémon that brings humans and Pokémon closer together!" Wes said.

"Pokémon were put in this world to serve humans!" Evice said.

"No, Pokémon were put in this world to live with humans. Pokémon aren't servants, accessories, or weapons! They're friends to humans, and we humans are their friends," Wes said.

"That's ridiculous nonsense! Pokémon are not people like us! They're just creatures made to our bidding! I came up with this Shadow Pokémon plan as a way to show the world of what Pokémon are capable of when they're emotionless creatures!" Evice said.

"So, that's why you made them shut the doors to their hearts? Well, it's a good thing I came around," Wes said.

"I will make you wish that you haven't! Tyranitar! Shadow Fire!" Evice ordered. Tyranitar fired a Shadow Fire at Espeon and Umbreon, so they both ran.

"This isn't good. Espeon's Psychic-type attacks won't touch Tyranitar since it's a Dark-type Pokémon. Umbreon's Dark-type moves won't do much either," Wes said in his thoughts. He then remembered the Master Ball. "Wait, the Master Ball. I could use it. I just have to keep Tyranitar and Evice distracted long enough to do it." He called out. "Keep running!" Espeon and Umbreon kept on running around.

"Aren't you going to attack me, boy? I have a feeling you're stalling? Stalling is a sign of weakness. So, I'm going to burn you, your Pokémon, and your beliefs down to the ground. But after I cool it off first. Shadow Chill!" Tyranitar unleashed Shadow Chill at Espeon and Umbreon. Rui knew what he was planning.

"I get it. Wes has Espeon and Umbreon distracting Tyranitar by running around, distracting Evice and Tyranitar long enough for Wes to get the Master Ball ready," Rui said in her thoughts.

"Just a little longer," Wes said under his breath.

"Shadow Bolt!" Evice ordered. Tyranitar unleashed Shadow Bolt, hitting Espeon and Umbreon. "Finish them both." Seeing that the moment was right, Wes took out the Master Ball and converted it into a Snag Ball. He threw the Master Ball, hitting Tyranitar, making it flow inside. The Master Ball wobbles around and around. Stars swirls around the Master Ball to confirm the catch, much to Evice's dismay.

"Yes!" Wes exclaimed.

"Yes!" Rui cheered.

"NO!" Evice roared. "No! Even my ultimate Pokémon was snagged from me!" Evice then realized Wes was tricking him with the running. "You tricked me! Damn you!"

"It was your own fault for being distracted, Evice," Wes said.

"It will not end this way, Wes. I will not forget nor forgive what you have done here today! I promise you that you will pay for everything you have done! I will exact my revenge on you!" Evice said. Just then, Duking, Silva, Eagun, Pikachu, Chief Sherles, Johnson, and Looker have arrived, along with a swarm of international police officers. He growled.

"Evice of Team Shadow, international police! You are under arrest for crimes against the Orre region, including illegal experimentation on Pokémon!" Looker announced.

"You have nowhere to go," Chief Sherles said.

"I think not," Evice said as a helicopter arrived to pick him up. He laughed evilly. "Team Shadow will begin the Shadow Pokémon project all over again. Like the darkness itself, you cannot stop us!"

"He's gonna get away!" Rui said.

"Stop him!" Wes said. They all tried to reach him as a rope ladder comes down for Evice to climb up.

"Master Evice, hurry!" The pilot said. Just then, a fireball came out of nowhere and heads right for the helicopter. "What the?!" He fireball hits the helicopter and it comes down. "Mayday! Mayday!" The helicopter makes a crash landing.

"No!" Evice exclaimed as Sherles and Johnson grabbed him and slapped the handcuffs on him. "What happened? Where did that come from?"

"I'm with him. What just happened?" Wes asked. He got his answer when Ho-Oh flew high above them.

"Is that what I think it is?" Duking asked.

"It is. It's the legendary Pokémon, Ho-Oh," Eagun said.

"It's beautiful," Silva said.

"Majestic," Duking said.

"Ho-Oh must have been watching over you two. It's obvious Ho-Oh was very displeased by the concept of Shadow Pokémon," Eagun said.

"That's why Ho-Oh did that. Ho-Oh didn't want Evice to escape and wanted Evice to pat for his crimes against Pokémon," Rui said.

"It makes sense," Wes said. "With Team Shadow defeated, the Shadow Pokémon project has officially been sunk. It will be anyway."

"I think I know what you mean, Wes," Rui said.

Looker, Sherles and Johnson took Evice and Team Shadow to be booked. Wes and Rui took Skarmory, Metagross, and Tyranitar to the Relic Stone to he purified. Wes blew on the Time Flute and Celebi appeared and purified the Shadow Pokémon, freeing them once and for all.

"Now, it is over," Wes said.

Meanwhile, the members of Organization XIII have gathered around.

"The Shadow Pokémon plan has failed, then?" Xemnas asked.

"Regrettably, Lord Xemnas. The last of the Shadow Pokémon have been purified," Saïx said.

"Well, it wasn't a total loss. We have a clue on who the meddlers are, and we will have to do something about it," Xigbar said.

"I agree. Wes and Rui have caused so much trouble for us, and it must be addressed," Xaldin said.

"And I know who's perfect for the task," Saïx said, setting his attention on Axel.

"Like I didn't know who you were gonna send out. I'll do it if it has to be that way," Axel said.

"Good Axel. You will depart at once. And you know the consequences for failure," Xemnas coldly stated.

"I'm on it," Axel said. He sighed to himself. He thinks to himself, "Why do I get stuck with all the icky jobs?" Axel took his leave through a corridor of darkness.

Elsewhere, a Keyblade floats in one of thirteen pedestals.

"So, it has begun. The first of 13 keys have been forged. Only time will tell when the other 12 will reveal themselves," a dark and calculating voice said.

Something tells me something is up. Who was that and what are these 13 keys? Maybe we might get an answer in the future, but the story doesn't end here. The next one does.