Back in Orre, Grey's friends have returned to their daily activities. Professor Krane and Lily continue to work on their Pokémon research. Jovi makes her usual trips to 's lab to "play" with Chobin and the Doctor. Michael is training at Mt Battle. Rui trains her "Shadow Seeker" powers with her Pokémon at the Relic Stone in Relic Forest. Wes travels around Orre fighting Team Snagem as his debt to society. Though there isn't a day that goes by that a thought of Grey doesn't pass through their minds.
One morning Lily is sitting in her kitchen drinking coffee. It has been a few days since she last talked to Grey and as any mother she is very worried. She looks out the window and she sees an Altaria swoop down. With its cloud like wings, the blue bird lands in front of the house. Rui jumps off its back. She fixes her hair then pulls out a pokeball from her bag and recalls her Altaria.
Lily gets up and walks to the door to let Rui in. "Hello there"
"Hey Lily." Rui says "How have you been?"
"I've been good." Lily says. "It's been quiet with Jack out of the house."
"Haha yeah Jovi has no one to annoy now." Rui laughs.
Lily leads Rui into the kitchen and offers her some coffee. They sit down and start some small talk. While they are talking, a picture catches Rui's eye. It is an old group picture of everyone. Rui, Wes, Michael, Jovi, Prof Krane, Lily and Grey. She picks up the picture. "This was the first time he was normal right?" asks Rui.
"Yeah" replies Lily "Remember the day you guys found him?"
"I will always remember that day." says Rui.
Flashback three years ago. Prof Krane had just sent Michael out deep into the desert. There had been reports on shady characters entering a base. With Eevee and an updated Snag Machine Michael was sent to clear out the base and look for any Shadow Pokémon. Michael looked at the Snag Machine. "It's been awhile since I wore this," "I hope nothing big is going down." He revved his scooter as he continued to the base.
Coming from the other direction was Wes and Rui. Wes had heard a few grunts in Pyrite Town talk something about Shadow Pokémon. He then commenced to beat the crap out of them until they told him everything.
Turned out a few ex Cipher Peons were gathering to restart Cipher with their new Shadow Pokémon creator code name Subject 51. So Wes and Rui saddled up and headed to the desert base.
Michael got to the base first. It was an abandoned hideout from Team Snagem. The windows were broken, and the door was ripped off. Over the years the sand had gathered up and swallowed up most of the outside of the hideout.
Michael hid his scooter behind some sand dunes near the hideout then walked into the base. He crept around inside. It was very dark and pipes were everywhere. The humidity was almost unbearable. Michael started to sweat as soon as he walked inside.
As he wandered around he heard something. "Hey what are you doing here?!" asked a voice. Michael turned around and saw a Cipher peon. His outfit was ripped and ragged. His helmet was cracked and had duct tape holding some parts together. "Is that a s-snag machine on your arm?!" asked the peon. Michael grinned as he grabbed two pokeballs from his belt.
"Here we go again." said Michael as he tossed out Eevee and Ursaring.
As Michael battled the Peon, Wes and Rui pull up in front of the base. "Metagross protect the bike." commanded Wes as he released Metagross from it's pokeball.
The two ran into the base and start to maneuver through it. While they wandered around, Michael had just snagged the Peon's Shadow Grovyle. The sounds of the battle lured Wes and Rui towards them. "I think it's over." said Rui.
"Then let see what happened." said Wes.
Wes and Rui finally made it to the battle scene. Michael stared at the new Shadow Grovyle he snagged. "I really hoped it wouldn't come to this."
Wes and Rui hid behind a wall so Michael couldn't see them. "Who is that Wes?" asked Rui.
"I don't know Rui," replied Wes "And I don't want to find out."
"So are we going to battle him?" asked Ru.
"No," replied Wes. He picked up a poll that was lying next to him. "We're going through him."
Wes snuck behind Michael, but just as he got close Eevee tackled Wes exposing him. "Who the hell are you?!" yelled Michael.
Wes crawled back "We should be asking you the same thing kid!" Rui ran over to help Wes up. "Rui is that Eevee a Shadow Pokémon?"
Rui stared at the Eevee examining every bit of it. "No it isn't a Shadow Pokémon Wes."
Michael looked puzzled. "You do know can't tell Shadow Pokémon from Regular Pokémon without an Aura Reader, right?"
"That shows what you know kid." said Wes
Michael looked at the couple for a few seconds. They were a young couple. A girl named Rui that said she can see Shadow Pokémon, and a guy named Wes with a weird contraption on his left arm that resembles a Snag Machine. Then it finally hit him. "You guys are Wes and Rui the Shadow Heros right?!"
"Yeah," said Wes "What's it to you?"
Michael held up his left arm with his Snag Machine. "My name is Michael I'm the third Shadow Hero!"
"You're the kid who saved Orre a year ago?" asked Wes as he got up.
"Yep that was me." gloated Michael.
Rui squealed in excitement "Hurray the three Shadow Heros are all together to bring down Cipher once more!"
Wes quickly covered Rui's mouth with his hand "Shut it Rui! Are you trying to get us caught?"
Rui removed herself from Wes' grip "Thats no way to talk to you girlfriend Wes" said Rui. She then kicked Wes in the balls before walking over to Michael. "That pokeball you're holding, it has a Shadow Pokémon in it right?"
"Yeah." said Michael "You can see the aura through the pokeball?"
"Yep." replied Rui. "What do you think I have been doing for the past eight years?"
"Um I don't know." said Michael.
"Okay now that we've gotten all chummy," said Wes as he was getting up "We got to get back to business. What do you know about Cipher being here?"
"Not much." said Michael. "There were reports about weird people around here so Prof Krane sent me to investigate."
"Okay that doesn't help at all." said Wes. "What do you know about Subject 51?"
"I don't know." said Michael. "It sounds very familiar, but now I got nothing."
"Kid you are no help at all." groaned Wes.
"Hey I'm the one who caught the Shadow Grovyle." stated Michael.
"Yeah because you were here first!" yelled Wes.
The two and now at each others throats arguing. "Will both of you shut up!" yelled Rui "We have a mission remember."
Wes and Michael stopped arguing and looked at each other. "Come on the guy ran this way." said Michael leading them down a hall.
The hall was dark and muggy. You can hear Rattatas scurrying around. At the end of the hall were two doors. The doors opened and three Cipher Peons were waiting. Their clothes looked as bad as the last one.
"Wow you guys look like shit." remarked Wes.
"Shut it." said a Cipher Peon. "You won't be saying that after we beat you to a pulp."
Both Michael and Wes grabbed two pokeball. "Three vs two," said Michael "We got this."
"No it's three vs three." said Rui as she pulled two pokeballs from the inside of her jacket.
"You sure you want to do this Rui?" asked Wes.
"Of course," said Rui "It's about time I help you in these battles."
"Alright," said Wes "Let's do this!"
Wes used Umbreon and Espeon. Michael used Flygon and Arcanine, and Rui used Plusle and Minum. The three Cipher Peons used a Marill, Haunter, Miltank, Shuckle, Nidorino, and Masquerain.
"Wes, Michael the Haunter, Nidorino and Masquerain are Shadow Pokémon!" yelled Rui.
"Ok Rui!" yelled Wes.
"Maril use Bubblebeam!" yelled a Peon. Marill fired a Bubblebeam at Arcanine.
"Arcanine dodge it!" yelled Michael.
"I don't think so," said another Peon "Haunter, Nidorino use Shadow Rush!"
Nidorino and Haunter striked Arcanine as she was avoiding Marill's attack.
"Ha you idiot!" laughed Wes "Umbreon use Crunch, Espeon use Physic!"
Umbreon charged Haunter, the yellow outlines on his body began to glow. Nidorino jumped in front of Haunter to take the attack. Espeon then jumped over Umbreon and fired her Psychic attack knocking Nidorino through Haunter into the wall knocking it out. Umbreon lunged at Hunter sinking his fangs into Haunter spectral body, both attacks were super effective.
Wes and Michael started to charge their snag balls. "Snag ball go! yelled Wes and Michael simultaneously.
The snag balls struck Nidorino and Hunter sucking them inside. The snag balls began to shake. The room was quite watching them. Wes' snag ball stopped first catching Hunter. Michael's snag ball with Nidorino shook for a few more seconds before it stopped.
"Plusle Thunder!" yelled Rui from across the room. Plusle launched a mighty Thunder attack striking Marill knocking it out while everyone was focused on Wes and Michael's duel snag.
"Hey that was unfair!" yelled the Peon.
"All's fair in love and war." said Rui giving a wink to the Peon.
The Peon began to blush as he stared at Rui. "Quick Flygon use Dragon Rush on Miltank, go!" commanded Michael. Flygon took flight at Miltank.
"Miltank use Defense Curl!" ordered a Peon but it was too late. Flygon had already struck Miltank and it was shot up into the air. It hit the ceiling then fell to the ground as dead weight.
"Four down two to go." said Wes
"Shit we can't lose." said the Peon. In a rage he commanded his Masquerain "Masquerain use Shadow Rush," he then pointed Rui "On the girl!"
Masquerain flew towards Rui. It maneuvered through all the Pokémon. Just as it was about to make contact with Rui, Wes jumped out in front taking the hit. He was knocked back into the wall. Now Michael is pissed. "Arcanine jump on Flygon's back!" yelled Michael.
The two Pokémon did what their master ordered. Michael ran over to Rui who is tending to Wes' body. He stood in front of them protecting the two from any further damage. "Now Flygon use Earthquake!" yelled Michael. Flygon lets loose an Earthquake that was off the richter scale. Shuckle bounced around the room like a rubber ball while Masquerain was not affected. A few pipes were shaken loose and were about to fall on Michael and the others. Umbreon and Espeon both used a Return attack breaking the pipes into a bunch of little pieces. "Thanks you two," "Now finish it Arcanine use Fire Blast!"
Arcanine jumped off of Flygon and fired an amazing Fire Blast. It was a critical hit and the Masquerain crumbled to the ground. Michael charged a snag ball. "You're mine, Snag Ball go!" yelled Michael as he lobbed the ball. Masquerain was sucked in and within seconds was caught.
"Shit." said one Peon.
"We got to get out of here." said another Peon.
"Let's." said the third. The three Peons then ran for their lives, but Michael didn't care he turned around to help Rui with Wes.
"Rui how is he?" asked Michael.
"I'm fine." said Wes. He got up pushing Rui off of him. He then shoved his way past Michael. Wes walking with a limp stops. "Kid you did a good job."
Michael smirked a little "Thanks."
Rui got up and walked over to Wes and Michael "Wes you hurt your leg you can't walk on it."
"We will worry about my leg later." said Wes. "Right now we need to find Subject 51 and snag it"
"You think Subject 51 is a Pokemon?" asked Michael.
"What else can it be." replied Wes. "Now lets go."
The rest of the walk was uninterrupted. The three didn't run into any Peons or Shadow Pokemon. Once they reached a dead end they heard something. "What the hell is that?" asked Wes.
"It sounds like a crying" said Rui.
"Wes I thought you would recognize that?" snickered Michael.
Wes smacked Michael in the back of the head. Rui's eyes glowed "I see a Shadow Pokémon on the other side of that wall."
"How many?" asked Wes.
"One," said Rui. "One Shadow Pokémon, and,"
"And what?" asked Michael.
"I don't know." said Rui "It has a shadow aura, but I can't make out the shape."
"Subject 51." said Wes.
"Then lets go." said Michael. Michael took out a pokeball and released Aggron. "Aggron take down that wall."
Aggron rammed into the wall a few times before she busted through it leaving a suitable hole for the three to walk through. As soon as they walked into the room they were attacked by a Pokémon. The Pokémon was a small Pokémon. It had shiny golden fur on one half of its body and the other half was black. It had big ears and on the tip of it's tail was a star shaped object.
"What the hell is that thing?" asked Wes.
"I don't know?" said Michael. "Maybe a new type of Pokémon."
"Score!" said Wes "That thing will sell at a high price once purified!"
Rui walked over and hit Wes "Will you shut it!"
The Pokémon lunged at the three while they were distracted.
"What the hell!" yelled Michael "Whose commanding it?"
"I don't know Michael." said Rui. "I didn't hear anything but that crying." Rui's eyes started to glow again. She saw a small figure through a wall of junk in the room. "There it is, the crying thing!"
The Pokémon looked scared, it turned around and ran back toward the object.
"It's retreating to Subject 51!" yelled Wes. "After it!"
The three chased the Pokémon down the room. They caught up and cornered the Pokémon in front of a door. "Now we got you Subject 51." said Wes with a charged Snag Ball in his hand. He flung open the door and sitting in front of him was a little boy that couldn't be older than seven.
"Aw how cute." said Rui. She went to pick him up but the Pokémon lunged at her protecting the boy. "Hey!"
"That's it!" said Michael. He charged a snag ball. "This little thing is mine!"
Wes smacked Michael's hand causing a misfire. Wes backed up and leaned against the wall with his hand. "Let's go." said Wes
"What do you mean let's go?" asked Michael. "What about the Pokémon?"
"And the kid?" asked Rui.
Wes was already walking away. Michael and Rui looked at each other, then the kid with the Pokémon, then back and each other before running after Wes.
Back outside the lab Wes had recalled his Metagross. Michael and Rui walked out of the base. "Wes what the hell was that about?" asked Michael.
"Yeah Wes we just left a Shadow Pokémon and a child in there." said Rui.
"I know." said Wes "I just need to see something." Wes walked over to his bike and pulled out a tablet. He pressed a few buttons and a live stream of the boy came up.
"How did you do that?" asked Michael.
"I placed a little camera on that wall I was leaning on." said Wes "I just want see something."
Michael, Wes and Rui watched the video feed. The boy was still crying and the Pokémon was trying to cheer him up. Finally it got the boy to smile that's when Wes paused it.
"Look at his eyes." said Wes "They're both dark purple"
Rui looked shocked. "Michael don't his eyes look like shadow aura?" asked Rui.
"Yea Rui they do." replied Michael.
Wes threw the tablet to the ground and ran back into the base. Rui and Michael chase after him.
"Wes where are you going?!" yelled Rui. Wes didn't answer he just kept running. When they finally reached the boy the Pokémon tried to attack them.
"I don't have time for you!" said Wes "Let's go Umbreon!"
When Umbreon was released the boy's eyes started glowing. Umbreon cried out in pain. "What's going on?!" yelled Wes.
Rui's eyes also begin to glow and Michael Aura Reader had been activated. "Wes recall Umbreon now!" said Rui "Do it now!"
Umbreon fell to the ground. He began to hyperventilate and cried out in pain louder.
"Rui what's happening?" asked Wes.
"He's turning Umbreon into a Shadow Pokémon!" yelled Michael.
Wes looked astonished he couldn't move all. All of the color had vanished from his face. His eyes were wide open and sweat dripped from his face. For the first time in years Wes was scared.
"Wes recall Umbreon!" yelled Rui.
Wes came to his senses and recalled Umbreon. He fell to his knees as he held the pokeball close to his chest. Rui ran over to comfort him.
The strange Pokémon was still growling at the three ready to attack.
"I've had enough of this thing." said Michael. He pulled an already charged snag ball from his pouch. "Snag Ball go!"
Michael threw the snag ball and the Pokémon was sucked in. The ball shook a few time before it stopped.
"Rui is he alright?" asked Wes.
Rui examined the pokeball. She smiled and said "Yes Umbreon will be alright Wes."
Wes smiled then looked down at the pokeball "I'm sorry Umbreon"
Michael walked over to the couple "So what about the kid?"
"We are taking him with us." said Rui.
"Yes we will take him with us." said Wes as he got up.
The three walk over to the boy. He had started crying again. Wes tried to comfort the boy but the boy just cried harder.
"Wes I don't think you're suitable to calm down a crying child" joked Michael.
"Oh and you are?" asked Wes.
"Well yes I am since I have a little sister about the same age." said Michael. He took the boy from Wes, but still couldn't calm him down.
"Oh look parent of the year." said Wes.
"Shut up." said Michael.
The boy began to cry harder because of the fighting between Michael and Wes.
"Both of you shut up, you both suck." said Rui. She took the boy from Michael. She held him for a few seconds and the boy just stopped. "Never let men do a womans job" giggled Rui.
"Alright now that's fixed now what?" asked Wes.
"Come back to the lab with me." said Michael. "My mom and Prof Krane can help us figure out what's wrong with the kid."
"Sounds like a plan." said Wes. "Lets go."