This is part two of my Cipher series. This takes place immediately after the battle for the Sinnoh League. Disclaimer: I do NOT own pokemon, or anything associated with it, so yeah, no suing please!

The Flames of Resistance

Chapter 1

May, a young brunette coordinator just barely past the age of fourteen wore an orange blouse with her black biker shorts underneath. She wore white gloves with black finger tips and had a green bandana with a white pokeball symbol on it tied on top of her head, causing her hair to form its signature style by coming down on the sides of her face. She also had a green fanny pack tied around her waist.

May clutched a boy in her arms, Alex. He had the same color hair and eyes as May, but his appearances greatly mimicked those of his father more than hers. He wore a torn white combat jacket with black pants. The boy looked extremely tired, and was breathing heavily, as if winded.

Standing over the two of them, Ash couldn't help but smile. He wore his Black vest with a yellow stripe crossing the vest horizontally down the middle. He wore baggy jeans and had a cap with a pokeball symbol on it. On his shoulder sat the loyal electric mouse, Pikachu. His yellow fur, covered in dirt and scraps, was soft to the touch.

"Mom, Can't… breathe," Alex forced out, just barely above a whisper to the girl holding him. May almost visibly jumped after hearing the first word.

'Mom?' she thought to herself. The last time she was called by that name was when she escorted Manaphy to the Sea Temple. May accepted that she would become the boy's mother over time, and the thought still brought a smile to her face, but she never once heard him call her that before. With a loving smile May held Alex tighter for a second before letting him breathe. Although she wasn't hugging him anymore, May still had him in her arms.

Alex tried to stand but after seeing that it was impossible, Alex gave in and let his future mother be his support beam. Ash dropped to his knees, took off his cap and put it on his son's head, pulling the bill down to cover his face, chuckling as he did so.

"I guess I'm too beat up to move on my own," Alex said mournfully as May pulled the bill of the hat up. Gardevoir, Alex's loyal embrace pokemon sat down next to her trainer and was about to try and heal some of his injuries. "Gardy, don't even try it, you're just as tired and beat up as I am," Alex said without even having to look at the Gardevoir.

"But, you're hurt," Gardevoir tried to reason.

"And you used all of your energy in that psycho-boost attack," Alex replied via telepathy.

Gardevoir began to say something else but Alex let his weariness get the better of him and drifted off to sleep. Using May's chest as a pillow and her heart beat as a lullaby, the last thing he saw before he let his dreams take him were his parent's shinning faces gleaming in the morning sun.

May was startled by the boy's actions, as well as the fact that she became his pillow, but quickly shook it off and her surprise was replaced by happiness. Ash gave his girlfriend a loving smile, which May graciously answered. He gave the girl a quick, chaste kiss on the lips causing her to blush, just the way he thought was adorable.

"Oh Ash Ketchum, what am I going to do with you?" May joked in a kind loving tone as she lightly shook her head, a smile on her face the entire time. Ash chuckled in response. Looking at the sleeping boy in her arms, May reached back into her bag for a pokeball. "Blazekin, can you please carry him for us?" May asked her starter pokemon. The tall fighting fire type, happily nodded its head before reaching down for the boy. Both Ash and May urged caution to the blaze pokemon as it carried the sleeping boy back to the downed drop ship.

As they traveled, slowly and carefully, Ash couldn't help but notice that the elderly lady that had stopped him and May just moments ago had completely disappeared.

"Emily, you are grounded!" Dawn roared at her daughter. Dawn yelled with such sheer force that everyone nearby had to cover their ears for fear of going deaf. Blue closed her eyes as well, fearing to look at her mother. Blue jumped in shock when she felt her mother's arms wrap around her small frame.

"Mom…" her voice trailed off.

"I was so worried for you, When I saw him holding you, I-" Dawn struggled to say, tears freely flowing from her eyes. "I thought I was going to lose you," the mother said as she buried her face in her daughter's hair. Blue began to cry as well, and returned her mother's hug.

Gary stood back watching the scene, a smile gracing his face. One of his soldiers approached him and snapped to a salute. Gary turned to face the troop and noticed how dirty his uniform was and all the scrapes and bruises he had. "Report," Gary said calmly.

"Sir! Red Team and Yellow Team have successfully cleared the city of all Cipher forces, and have linked up with the rest of blue team. If you want I can-," the man was cut off.

"Why don't you let us explain while you go and get patched up, Brock said, causing the troop to turn and salute to the other team leaders as well. The soldier nodded and scampered off to the field hospital.

"Misty, Tracy, I have some bad news for you," Gary said to two of the new arrivals. Both Misty and Gary shared a glance with each other before turning back to Gary, curious expressions on their faces.

"There," a young blonde girl said as she finished wrapping up one of the injured soldiers. Her long blonde hair had been tied up into a bun, and she whipped the sweat off of her face. She wore a plain black sweater with a long black skirt. She wore a yellow apron over her clothes. She had emerald green eyes that glistened with kindness.

Ever since being ushered in the place, Yellow had decided to help out the overwhelmed Chancy with their work load by becoming a make-shift nurse. Her older brother, Lucas decided to help too.

Lucas wore a black and grey vest with a red scarf and a red had. He wore simple jeans with his outfit. His eyes were a calm baby blue, and his hair was a dark green. Lucas too, was exhausted, they had treated nearly a hundred patients already, and many more had been helped by the Chancy.

Turning to see his little sister, Lucas was surprised to see all the color fade from Yellow's face as her eyes went wide. Then he felt as if a murderous shadow had engulfed him. "Mom is right behind me isn't she?" he asked the blonde.

Before Yellow could reply, some else did. "You're damn right I am!" the voice roared. Lucas turned to face his mother, his face paled knowing just how much trouble they were in. "What were you thinking!" Misty roared. "Didn't you think how dangerous it would be!"

Both children shifted their gaze to the ground. "I can explain mom-" Yellow started.

"It's my fault mom," Lucas cut her off, earning a surprised glance from his little sister. "I talked Tiff into coming, if it wasn't because of me, she wouldn't have come." Misty ran her eyes over her children, seeing that they were completely unharmed she released the breath that she had been holding.

"Lucas, you're grounded for the rest of the month, no pokemon battles or training at all," Misty said as she narrowed her glare to her son.

"(Please don't be so hard on them, they were a great help!)" one of the Chancy came to the rescue. The other nodded in agreement. Both Tiffany and Lucas gave their mother the most powerful puppy-dog looks they could muster.

"Fine, you can train but you're still grounded!" Misty said as she left the ship to finish her report.

"Did anyone hear from Green Team yet?" Gary asked. The others looked at each other before turning to face Gary.

"I didn't hear anything from them, do you suppose it's possible that they got ambushed?" Brock asked, crossing his arms. Gary shook his head.

"No, I doubt it, and even if they were, they would have said something," Gary replied.

As if on cue, the sounds of the Resistance drop ships' engines could be heard in the distance. The six leaders turned to see fifteen large crafts descend just outside the city.

"Speak of the Houndoom," Riche said.

A few minutes later, both Max and Paul walked into the stadium and greeted the rest of their comrades. "What happened to the city?" Max asked

"Cipher happened. Now why didn't you check in?" Gary asked rather harshly.

"When we heard the radio transmission, we made best speed here, but decided to go quiet in case they may have hacked our radio frequency," Paul answered coldly. "In case you were ambushed, we could get as close as possible before we would get spotted."

Gary nodded in approval. "So, where is he? Is Alex alright?" Max asked. "Where's my nephew?"

"Alex is here, they didn't get him," Gary replied shifting his gaze towards the make shift field hospital.

"So the mission was a success?" Tracy asked, relief in his voice. Gary shook his head, earning questioning looks from the others.

"We rescued Alex in time, but I'm afraid my daughter's involvement caused him to go into reverse mode," Gary said.

"So it's true then, Alex is a shadow," Brock said sadly.

"How!" Max exclaimed. "How is this even possible? Only pokemon can become shadows? How did they manage to turn a human into one, and when!" he continued.

"I don't know Max," Gary answered, his eyes cast downward.

"Regardless of how, I want to know when it happened," Misty said. "When could they have contaminated him?"

"Contaminated?" Max spat at Misty, the venom in his voice apparent. "My nephew is not contaminated like some plague ridden-!" Max started to yell. Misty was taken aback.

"You're right, I'm sorry," Misty apologized.

"Max, you're absolutely right, although this is serious, we can't just treat him differently, it may induce another reverse mode," Brock said with a nod. "But at the same time, we don't know if it's going to have any side effects."

"Never the less, he is sick, and that isn't a good thing when it comes to war," Gary added.

Everyone's eyes widened. "You don't mean…" Tracy started.

"Until it's confirmed we cannot do anything, but deep down in my gut, I can't help but dread that we just started the war," Gary said.

"Well, in the meantime I'm going to see if I can make any repairs to your ship," Tracy suggested as he made his way to the downed drop ship.

"(Other than a few broken ribs, and a sprained ankle, he should be fine!)" Chancy said as it finished scanning the unconscious boy. Ash sighed in relief and May smiled calmly. The other Chancy was being helped by Yellow as they were taking care of their pokemon. Lucas was running around the room fetching all of the tools or items that the medics needed.

Chancy placed its hands just over Alex's chest, and a soft pulsing light emanated from them. Both Ash and May watched as Chancy preformed heal bell on their future son. "(There, as good as new!)" Chancy beamed as it wrapped the boy's right foot in a brace.

"Thank you Chancy," May said thankfully. Ash smiled gratefully. Lucas handed a pair of crutches to Ash.

"He'll need these," he said before going back to getting medicines for the pokemon.

Gardevoir, having been the first one restored back to full health took one look at the crutches. "I don't think so," she said as she used her healing abilities to finish healing her trainer. Seeing as how most of the work was done for her, Gardevoir finished in just a few seconds.

"You know, this is only the second time he's slept in the past week, it's good to see that I didn't have to put him to sleep this time, perhaps things will go back to normal now," Gardy sighed. The embrace pokemon ignored the nervous, pleading look from May, the girl was hoping for an explanation, but Gardevoir decided to wait till her trainer woke up.

It was a few hours later that Alex finally woke from his slumber. He took a glance around and found Ash and May snuggled up, sleeping on one side of his stretcher, and Emily on the other side. Gardevoir was awake keeping a firm watch over them. Further off, Yellow seemed to have passed out in a chair, using the metal wall as her pillow.

He felt Gardevoir slowly wrap her mind around his, in a more calming way than usual. Alex soon feared that she knew his secret, and tried to find a way to best approach the topic.

Suddenly Lucas burst through the entrance, a sense of urgency about him. "You guys! You've got to see this!" he shouted, causing everyone to jump.

"Oww, my head," Yellow mumbled as she rubbed the top of her head. Her startled awakening caused her to hit her head against the low ceiling. Both Ash and May grumbled about being woken up in such a rude manner. Blue simply rubbed her eyes open, before noticing that Alex was awake.

"Hey Blue," Ash started but started laughing when he turned to face the girl. Hearing Ash laugh, May turned as well and couldn't help but giggle.

Blue had Alex in a death grip hug, nuzzling him affectionately as he cast the others a pleading glance. While the two teens continued to share their amusement, Gardevoir released a sigh and used her psychic powers to separate the two from the one sided hug.

Blue cast the embrace pokemon a dirty look, to which Gardevoir shook off with a shrug. Alex immediately sprang to his feet ready to go see whatever it was that Lucas was so intent on showing everyone with his Gardevoir at his side. Blue quickly rose to follow and was immediately followed by both Ash and May. Pikachu, who had regrouped with his trainer after being healed sat on his usual spot located on Ash's shoulder. Yellow followed shortly after fixing her ruffled hair.

"…Leader," After this radio broadcast, severe fighting had been reported near the vicinity of the site of the Sinnoh League, set to take place in a few months," The news reporter said.

Gary and the others had gathered around the many televisions spread throughout the inside of the stadium, anxiously waiting for the news. He turned when the sounds of footsteps rang in his ears. He saw the children running to see what was going on. To his surprise, his godson was up and about. He smirked, Max noticed and followed his gaze, then had a smile of his own.

"As you can see," the news reporter continued. "The damage is extensive stretching all the way from the shore line to the stadium," she continued as the view showed footage of the battle's aftermath in the city. "We are unable to get any closer to the stadium from here as there still seems to be a large military presence here. However, many of the local citizens had given testimonies about what has transpired here."

"According to the locals, at about this time yesterday morning, a group of villainous thugs that go by the name of Cipher arrived and quickly seized the city before any formal resistance could be mounted. Then another group appeared, one individual at first, but soon after an army came and liberated the city with help from the locals. The locals had become hostages, forced to watch a one-on-one battle," The reporter continued. "Here with us now is Officer Jenny," the reporter added as she handed the microphone to the police officer.

"Thank you Diane," Jenny said. "According to our reports, Cipher is a criminal organization founded near the Orre Region. They first appeared about seven years ago, but where quickly put down by a renegade from a rival organization "Team Snagem" it was believed that this disbanded both organizations. However, about two years ago, Cipher came back with greater force, but was put down again by a boy from the local research institute. However, although the original head of Cipher is still behind bars, we are unsure who is running the group now, if anyone has any information, it would be greatly appreciated," Officer Jenny concluded as she handed the microphone back to the reporter.

"Thank you Officer Jenny," Diane, the news reporter said. "These crooks, Cipher, apparently disappeared shortly before dawn, so we were unable to see exactly which direction they went. We hope to have more information to you shortly," Diane finished. "Back to you Ted," she added. The view switched from the news reporter to the main news station.

Gary quickly turned the television off and released an audible sigh. "Well that's a relief," Brock said. The others nodded in agreement.

Alex stood, his face paled. Images of the destruction around the city kept replaying in his head, all of the bodies, Cipher and Resistance alike fresh in his mind."What have I done?" he quietly asked himself. His composure failing him as his grief took over. His arms began to shake as he tried to force tears back. "My selfish actions caused so much harm, what have I done?" he asked again, his voice just over a whisper this time.

The others all turned and looked at him sympathetically. Paul looked at him with a hard glance. "So what? What are you going to do about it? Cry?" Paul argued. Everyone looked back at him, disbelief in their eyes.

"Paul," Misty started.

"So some people gave their lives, it was to make sure you were safe," Paul continued. "If not because they care about you, then to keep you from falling into their hands. If Cipher got their hands on you, not only would the location of our headquarters be at risk, but also all of our comm. Frequencies, strategies, troop deployments, as well as whatever is in Orre that you're so persistent on protecting."

Alex looked up from the floor tiles to Paul's face. The purple haired trainer continued to glare at him. "Not to mention your… condition," he added. Alex flinched and looked at him with fear in his eyes. The other teenagers all looked between the two completely confused.

Gardevoir finally put all the pieces of the puzzle together Her trainer being so different, so emotional, Mistress Bella's strange instructions, Alex's special training, it was all to make a stand against himself. The black acid like substance she saw in his mindscape, she now knew what it was. Her trainer was pushing her away, to protect her from his shadow. 'That's why he wouldn't let me combine our minds!' she concluded to herself. She felt so sad for her trainer, to which she felt the emotion tenfold from his grief through their bond. She felt terrible, he was suffering for such a long time, and she didn't even notice, and she couldn't do anything about it.

"How long-?" Alex struggled to ask.

"Long enough for you to disappear and try to play mister hero," Paul reprimanded.

Alex suddenly let out a soft chuckle. "Thanks Paul, you just helped me realize something," he said. Paul raised an eyebrow as everyone else watched the transaction between them. "You made me realize, I played right into their trap, and if you guys hadn't come to get me, well…" his voice trailed off. He turned to face Gary. "Gary, I hereby resign from my position as Commander of the Resistance, and appoint you its leader until you deem my parents fit for the task," He finished.

Gary was taken aback, as were the others. Both Ash and May were completely shocked, not only were they going to have to run this army, but their son was running it the whole time.

Chapter one of The Flames of Resistance, the second part in my Cipher series.

AN: the chapters won't be as long as they were in The Dark Reign of Cipher, but there will be more of them.

Anyway, R&R your feedback is greatly appreciated!