Chapter 2

Three small rocks were tossed high into the air.

"Jolteon, use Thunderbolt!" Michael shouted.

A blast of lightning shot and zapped the first rock. Then a second blast hit the next rock followed by a third, which took out the last one.

Michael praised his Pokémon for his accuracy. He then turned to his sister who was standing with Plusey and Mimi. "See, Jovi. That is how you pull off a solid Thunderbolt. Now you try."

"Ok, big brother," she said as she took two larger rocks that she got from Michael. She tossed one of them up. "Go, Plusey, use Spark," Jovi said. Plusey waited patiently for the rock to come down and when it was close enough, Plusey jumped up and smashed the rock. It flew across the area.

Michael was impressed. Jovi had only been training for a little more than a week now and she already knew how to command her Pokémon. It also helped that Michael was being her tutor.

After a while, Jovi took a break with her Pokémon which gave Michael some time to work with Jolteon for a bit. He picked up a log that was about the size of his forearm. He threw it out so that it spun and flew decently far. "Go Jolteon, use Thunder Fang." Jolteon took off and as he ran for the stick, he teeth were charged with electricity. Jolteon jumped up and bit into the stick and landed with it in his jaws. It was basically fetch but it was also great training for taking down a fast Flying Pokémon.

"Good job, Jolteon," Michael said as he petted his best friend.

"Jolt. Jolt," the Pokémon replied.

"That was a perfect Thunder Fang," said Professor Krane as he watched from the door of the Lab. He came down the steps and walked out to meet Jak. "Jolteon hasn't lost an ounce of skill since the whole ordeal with Cipher."

"Training keeps us on our toes," Michael said. "Right, Jolteon?"

"JOLT-EON!" the Pokémon said.

Michael stood up to talk to Krane. "So what's up, Professor?"

"I got a call from Sheriff Sherles in Pyrite Town and we got a bit of an issue," the professor said.

"What issue?" Michael questioned.

"It appears that unknown men have broken into the Shadow Pokémon Lab in the middle of the desert."

"Cipher," Michael responded.

"We think so but we want you to check it out just in case," the Professor said, "They might be prepared so I suggest that you bring some other Pokémon with you."

000

Michael checked the fuel gauge on his scooter and then tweaked the hover matrix that was installed. Everything seemed in order. He took out three Pokéballs that he would bring with him. He had his Jolteon obviously and then he brought his Typhlosion that he evolved from when it was a Cyndaquil that he won at Mt. Battle and a Tyranitar that he originally got as a Larvitar from Duking in Pyrite Town. They were the three Pokémon that Michael thought would be the best for this. He put the Pokéballs back in his pocket and pulled his scooter out front. Professor Krane was there waiting with one of his aides.

"Remember, just find out what they are doing. Don't battle unless you have to. Battling would just attract attention."

Michael nodded in response.

"May I see your P*DA, Michael?" Krane asked.

Michael handed the professor the device and Krane added something into the USB slot on the side.

"I'm installing a Wireless communication system," the professor said when he handed the P*DA back to Michael. "Here, if you wear this ear piece, we can communicate more effectively."

Michael put on the ear piece and mounted his scooter.

"Good luck, Michael," Krane said.

Michael smiled as he zoomed off, heading towards the Shadow Pokémon Lab.

000

The majority of the Orre region was desert. The only exception to this was the northwestern part of the region which was actually a lush forest. But as luck would have it, the Shadow Pokemon Lab was in the middle of the desert. Being a desert, sandstorms were actually pretty common. Michael pulled up his goggles as to keep some of his vision. He got to the lab and he parked his scooter behind the lab so that no one would be able to find it. He made his way into the lab and he found that the door to the lab was actually wide open, as opposed to being locked with a code, which was normally how it was. Someone was definitely here. Michael proceeded down the elevator and he was prepared for the worst.

The elevator door opened and Michael hugged the wall. He snuck through, fearing that Cipher agents were swarming the place. After, sneaking around the halls for a bit, Michael was shocked to see no other living beings in the lab. This was weird. If men snuck into the lab, then where were they?

Michael went deeper into the lab and he entered one of the research rooms. Michael was shocked to find all of the equipment gone. Michael went into a conference room in the lab and he checked one of the filing cabinets and all of the files there were gone too.

After wandering a bit more and finding every single room, empty, Michael was really confused.

"Professor, do you copy?" Michael asked.

"I'm here, Michael. What could you find?" the professor replied on the other end.

"I've searched the entire Pokémon Lab and there is no one here. But they were obviously here and they were looking for something. All of the lab equipment and all of the data and files on Shadow Pokémon are missing."

"Well, that's not good," the professor replied. "Ok Michael, come back and we'll think of our next move."

Michael nodded as he left the room.

000

The Purify Chamber hasn't seen much use since the days of the Shadow Pokémon Crisis. The machines that were dead silent for a few years were suddenly powered up and came to life. The professor gave a sigh of relief, pleased that everything was working properly. Knowing that the Shadow Pokémon Project was about to be rebooted, Krane didn't really want to have to replace parts for the Purify Chamber.

The staff of the Pokémon HQ Lab including Krane, and Michael's mom, Lily, crammed into the conference room. They waited for Michael's return. Michael returned and he stood near the center of the room with his mother and Krane.

"Thank you all for coming here," Krane said.

"What is going on, professor?" an aide asked.

"Yesterday, some men entered the Shadow Pokémon Labe in the desert. When Michael checked the lab, the men were nowhere to be found, along with all the information and equipment in the lab."

"Wasn't that lab supposed to be destroyed?" another aide shouted.

"Yes, under order of the major leaders of Orre, demolition of the Shadow Pokémon Lab was scheduled to happen next week.

"That explains why they stole the equipment and information before the Lab would be destroyed, along with everything in it," Lily said.

"Exactly," Krane responded.

"Well, if the Shadow Pokémon Project is going to become active again, why aren't we searching to find these guys?" another aide shouted.

"We could search the entire Orre Region. We could even search the other regions in the world but that would take time. Time that we don't have," Krane replied.

"Well, why not have Michael stop them? He did it last time," an aide shouted asked.

"True, Michael is the best Trainer that we have at the HQ Lab," Lily stated.

"Yes, Michael is a talented Trainer but we don't know how big an operation this is. I don't want him charging recklessly into danger. On top of that, the Snag Machine is out of commission," Krane said.

The aides were appalled. It was horrible timing for the Snag Machine to malfunction like this but it would take a while to get the parts necessary to repair the device.

"Well, if he finds the criminals before any more Shadow Pokémon are made, then there won't be a need for the Snag Machine," Lily said.

Lily had a good point but that meant that the criminals would have to be found fast. "That is a good point but if these people were clever enough to steal an entire Lab full of valuable equipment and information then they will no doubt be prepared for Michael."

"What if we had another trainer that could help Michael find them?" an aide said.

"Another Trainer to watch his back?" Krane asked. "Well then I suppose that it could work. However, he or she would have to be just as talented as Michael or even more so but I don't know of a Trainer like that here."

Michael then got an idea. "How about the Hero?" Michael asked. His statement started to raise a small commotion between the aides that were present. Krane turned to Lily who suddenly looked down, depressed.

"Michael no one has seen hide or hair of the legendary Hero for 6 years," Krane said.

"I can go find him. He has to somewhere in Orre. And while I am out searching for him, I can also look for the criminals. Plus, he should still have the old Snag Machine so we can use that if we find any more Shadow Pokémon," Michael said.

The aides nodded in agreement.

Krane's eyes met with Lily's. He then turned to the aides. "It is probably one of the best ideas that we will get. We shall discuss the idea. You all are dismissed. Back to work," Krane said. The professor then turned to Michael. "Can you give us a second, Michael?"

The boy nodded and left with the aides.

Krane was alone with Lily. The Hero left him and Lily 6 years ago after the HQ Lab was built and since then, no one has heard from him. Would he even still be out there in Orre? If he was then, it would be a matter of finding him. Although, if anyone could find him, Michael could. And if anyone could help Michael stop these criminals, it would be the hero. "What do you think of Michael's plan?"

"He has been gone for 6 years. All that we went through and it feels like he just left me forever," Lily said.

"You know why he left," Krane said.

"I know I do," Lily said.

Begin Flashback

The shining white walls of the new Pokémon HQ Lab reflected the orange sunset that was cast on the area. Back then, her name wasn't Lily, it was Rui. She had a pink top on with jeans and white sneakers. She had a small black duffel bag in her hands as she carried it out to the orange motorcycle that was parked outside the Lab. She put the bag in the sidecar seat and turned around. Her husband for a year and a half, Wes, came outside. He was wearing his normal field gear: his long blue trench coat that covered his black plants and shoes. His silver hair blew in the wind. He was followed by his Espeon and Umbreon. His two loyal Pokémon that were with him before Wes went on his journey. He came over to the bike and Rui.

"I don't want you to go," she said.

"I wish I didn't have to but, I can't let more evil people destroy the lives of innocent Pokémon like Cipher did," Wes replied.

Rui nodded and looked down. A small tear escaped her eye. Wes hugged his wife and held her tight. "I'll be back before you know it."

A younger Krane then came out of the lab. He was holding a laptop in his hands. He came over to Wes and showed him the screen. "Ok, Wes, according to the evidence we got, if you head out north of Eclo Canyon, you should be able to find these men."

Wes nodded and mounted his motorcycle. He turned to Krane. "Take care of Rui."

Krane nodded and Wes turned to his wife. He kissed his softly on the lips. "I'll be home soon. Don't worry."

Then Wes started up his motorcycle and before Rui knew it, he was gone.

End Flashback

But Wes had been gone for six years. How could Lily not worry?

"Lily?" Krane asked, "Lily?"

Michael's mother snapped back into reality and looked at the professor. "Krane, he has been gone for six years. He is probably dead."

"You don't know that. Wes is a fighter. He wouldn't go down without a fight," Krane responded.

Lily was silent. Krane was right. Wes was very tough. No one could stop Wes when they were saving Orre together.

"Whether Wes is still out there or not, it wouldn't hurt for Michael to go out and find him. Maybe, Michael could find him and bring him back home," Krane explained.

Lily looked as a bit of home filled her heart.

"And if Michael doesn't find Wes, then he will find these unknown criminals first. The way I see it, there isn't any point in the kid just sitting here."

Lily nodded. "I agree, and Michael will need his father's help to stop these people."