Note: I don't own Pokemon, I just like the games.

Hidden Conflict

Summary: On the surface it appears that there's peace in the Kanto region. But under the surface, there is a war between the terrorist group known as The New World, and the Kantian Armed Forces. Using tactics and genetic experiments in ways no one ever thought possible, the New World threaten not only peace... but all humanity itself! Can the Saber and Lunar Teams survive the war and bring peace back to Kanto?

Chapter 01: The Raging Storm

KANTO DEFENSE AGENCY DATA ARCHIVE

RETRIEVING FILE #043253201

DATE: 05/30

LOCATION: Pewter City, Kanto 0900 HOURS

BEGINNING TRANSMISSON…

"This just in, it appears that the president is here in Pewter and about to give a press conference concerning the 'New World' terrorist organization." An anchorwoman says as the usually showing of Saturday morning cartoons was interrupted by a news flash. "We now go live to Marcus Tyler, who is there on the scene. Marcus?"

"Well, Kate, it looks as if the president has something very important to tell us as he asked to call a televised press conference. The reasons as to exactly why he called for this conference are still unclear, but there are some people who claim that this conference is about the war in Orre and to dispel the rumors concerning the New World terrorist group's return." A Professional looking news reporter said, from in front of a stage in front of the Pewter City Gym.

Suddenly the buzz and excitement that was in the air not too long ago was silenced, as the president of the Kanto Republic went on the stage and took the podium. "Ladies and gentlemen of the press…" one of his assistants said. "The president of the Kanto Republic."

"Thank you," President Dellnor said. "Ladies and gentlemen, I would like to thank you all for coming here today. I know it seems odd that I would want to call a press conference so suddenly, but I must assure all Kantians that the 'New World' threat is gone. They were defeated, overthrown, and destroyed thanks to the brave men and women in our armed forces and the Orren underground movement. They will not ever be coming be back. Also on that note, the armed forces in Orre assure me that Last of their forces will be defeated in a matter of weeks."

After the president finished his speech he was bombarded with hundreds of different questions. Some of them were "Mr. President, sir, do you think it's possible for the New World to return?" or "Mr. President, How is the situation in Orre, now? Has the situation improved at all?"

All these questions were put to rest we the president rose his hands to quiet the crowd down and get their attention. "Let me assure you all. The rumors concerning the New World's revival are indeed false, and there is absolutely nothing to worry about." However, the reporters continued to ask questions about the New World and Orre… specially about the rumors of their genetic experiments.

DATE: 05/30

LOCATION: 20 miles south of the Cinnabar Shore 2200 Hours

A lone Black Hawk military helicopter, with the Kantian insignia on the side of the vehicle, flies south through a harsh storm. Its destination? A cargo chip coming into the Cinnabar port. Inside the chopper are two pilots, two gunners behind 120mm mini-guns and a squad of Kantian soldiers armed with silenced assault rifles and sub-machine guns. The soldiers all had on black uniforms, with dark vests, and gas masks on the top of their heads. Four of the agents were male, and the other one and the lieutenant were both female. The ride was surprisingly quiet excusing the roar of the helicopter's rotors.

Everyone had the same question on their minds, but no one would dare ask the lieutenant on board. After a few minutes of silence, one of the agents finally spoke up. "Hey, lieutenant, didn't the president say that the war was over?" A scarlet eyed, young teenage girl asked. "Yes, he did." their commanding officer replied.

"So, then why are we here, in the middle of the Korren Ocean?" "Because, the press the conference was a way to keep the public from worrying." The pink haired, blue eyed lieutenant responded. "Also we are under direct order from both the president and General Greenfield to attack the cargo ship you were briefed about." The agents on board were a little confused. "Keep them from worrying? Ma'am… are you saying that the government's lying about our war with the New World?" the sergeant asked in a light British accent. "You act like this is the first time." She calmly said.

Before the sergeant could reply, however, "Heads up! I've got visual on the target." One of the pilots suddenly shouted. "ETA: two minutes and closing." There was movement inside the chopper as the agents prepared themselves. "Okay, agents listen up! Quick briefing, there are very important documents and precious cargo on that ship." The lieutenant shouted over the roar of the rotors. "We have to go in, kill all enemy soldiers on that ship, find the documents and cargo, and get out. Any questions?" "I have one, Ma'am," the sergeant said. "Any Intel on the hostiles on board?"

"Sixty seconds! Going dark." The pilot said as he turned off the search light on the nose of the Black Hawk, and shut off almost all lights inside the chopper. "Lightly armed, worst they have to offer us are AK-47s." She replied as she along with the rest of the team began to put on their gas masks, and checked their gear. "Switching radio commutations to a secure channel."

"I meant are they human or are they-?" "Thirty seconds!" The pilot yelled. The lieutenant just looked at the sergeant with a smile hidden under her mask. "I guess we're about to find out." She replied "Ten seconds." The helicopter hovered over the ship and steadied itself.

"Down the ropes, Sabers!" Two Saber Team members, followed by the lieutenant slid down the rope and landed just outside of the ship's controls room. "Weapons free." She whispered over the communication link, as the people inside the room noticed them. In no time they we gunned down by silenced weapons, be they could pull out their weapons, or get any help.

"Bridge is secure. Saber 1, you and the rest of the team stay in the chopper, Saber 5, Saber 7 and I will check the crew's quarters and radio in when it's clear." The lieutenant said, as she opened the door to the control room and entered followed by Sabers 5 and 7. "Roger that." Saber 1 replied. "Echo 17 to Alpha 3, be advised we are low on fuel. We cannot stay here for very long." One of the pilots said over the com. "I'm well aware of that, Echo 17. Don't worry, this'll be quick."

They quietly went down the stairs to find two guards walking up the hall. They were right behind the guards, so they didn't see them come down the stairs, nor did they notice Saber 5 as he sunck up behind them, shoot one in the head with a M9 with a silencer attachment and stabbed the other in his neck with a combat knife. "Way to go ninja boy." Saber 7 silently cheered her teammate.

"Good job. Let's go, we still have rooms to clear." Their commanding officer said. "Spilt up, and clear the crew's quarters. Any hostiles you see, drop on sight." "Copy that! They are so screwed." Saber 7 said as she went down the hallway on the right. Saber 5, however, did not reply. He just went down the hall opposite to Saber 7's. "Okay then. I'll just check the two rooms in front of me."

They slowly and quietly cleared the rest of the rooms. Most of the bad guys were asleep, so it was easy to kill them. But some of the others, who were awake as patrolling the halls, weren't as easy to kill. When Saber 7 finally found the documents they were looking for, a guard surprised her, knocked her weapon out of her hands, knocked her down to the floor and was about to tear her body apart with a shotgun.

Lucky for her, Saber 5 was right behind him. He quickly opened a pocket on his tactical vest, and tossed a kunai. In a matter of seconds, the kunai sailed throw the air and entered the neck of the enemy agents. Killing him almost instantly. "You're so reckless, you know that?" Saber 7's fear was quickly replaced with surprise, then disgust. "You actually brought your kunai throwing knifes? And you wonder why I call you 'Ninja Boy.'" She said to her teammate as grabbed her weapon that was next to the dead body and got back up. "It worked didn't it?" Saber 5 said balancing another kunai on the tip of his index finger.

"Whatever, Alpha 3," Saber 7 whispered into her com. "I found the documents that we came here for." "Splendid," Alpha 3 responded. "Make sure the rest of the rooms are secure before you leave." "Copy that!"

The rooms that the lieutenant had to clear were filled with sleeping tangos. All she had to do was shoot them in the head with her silenced M4A1 assault rifle. Some of the hostiles did move a bit, and one or two of them did opened eyes, but by the time they realized she was there, it was already too late. "This is just too easy." She whispered to herself, as she killed the last sleeping agent.

"This is Alpha 3 to all Saber Team members. The control room and the crew's quarters are both clear." She said in the com. "Regroup on deck." In a couple of minutes, Alpha 3, Saber 5 and Saber 7 were waiting on deck for their back up. Not too long after regrouping, a rope fell from the Black Hawk and the rest of the Saber Team slid down the rope and met up the with team one.

"Saber 1, ready for action ma'am." The sergeant said. "Saber 12 awaiting orders." A young corporal said as he took cover behind the edge of a metal container and looked over the side. "Saber 11, ready and raring to go." Another young agent said as he loaded his MP5 submachine gun. "Splendid, all units fan out. Stay four feet apart from each other." The team slowly went towards the back of the ship were the entrance to the cargo bay was. Whatever they were looking for was down below, heavily guarded.

They silence was suddenly broken when hostile forces from inside the second floor cabin windows, opened fire. The team quickly scrambled to cover positions. "Damn! How the hell did they smell us out?" "That's unimportant, Eleven! Now shut your yap and fire back!" Saber 1 shouted. "Hold your fire, Sabers." Alpha 3 calmly said, dispute their situation. "What? Ma'am are you saying that we just sit here and wait to get shot?! With due respect ma'am, that's insanity!" She didn't reply to twelve's remark. "Echo 17?" "We got 'em, standby." The Black Hawk helicopter past by the second story window, were the enemy was firing from, and a gunner on board fired his 120mm mini-guns at the bad guys, literately tearing them apart.

"That had to hurt!" the gunner enthusiastically shouted. "Alpha 3, we're at bingo fuel. We're bugging out." Echo 17 said over the com. "Both War Pelipper and Sea knight 10 will be on station for evac." "Copy that. Sabers, we still have a mission on our hands, move out!" "Ma'am!" The agents shouted as they got out from cover and hurried after their leader. "Sergeant! You and the corporal will stay here and wait for our ride home." "Understood." Saber 1 said. "Corporal?" "Yeah, I got. We stay behind, while you guys have all the fun… so unfair." Saber 12 sighed.

"Seven, Five, and Eleven with me." Alpha 3 said as she opened the door leading to their objective. "Yes, Ma'am!" the agents said. As they quietly went in, Saber 11 slung his SMG around his back, and took out a shotgun. "What the…? You can't be serious." "What? I like to keep this for close encounters." Saber 11 said with the pump of his shotgun.

"Whatever." Saber 7 said as she removed the silence suppressor from the end barrel of her assault rifle. Alpha 3 did the same thing with her gun, but Saber 5 on the other hand kept his MP5 SMG silenced. "Hey ninja boy! We could take the silencers off now." "I think I'll keep mine on." He emotionlessly said. "Why? I mean sure no one can hear you gun, but its power is decreased. Making it harder to kill the enemy." Seven explained. "I'll take my chances." Five replied.

"Clear, let's move up." Alpha 3 said as they slowly moved through the hall. "Saber 7, check the staircase for tango." "Copy that. You guys better watch my six." She said as the slowly moved toward the stairs. "Stairs clear." Seven reported. "I'm moving up." The others followed her down the stair, and trough the hallway. They stopped at the end of the corridor and pinned themselves against the wall. "Saber, Check the next corridor for hostiles." The lieutenant ordered. "Yes Ma'am." Saber 7 stuck her head out for about a second or two then immediately went back to cover as a wave of bullets came at her.

"Ma'am! They know we're here!" Seven shouted. "Naw, really? I couldn't tell." Saber 11 sarcastically remarked. "And here I thought they were aiming for the wall, but we're getting in their way." "Eleven I swear to God, if you don't shut the hell up, I'll shove a grenade so far up your ass, you'll be coughing up shrapnel for the rest of your life!" "Saber 7, Calm down and get ready, I'm going to throw a flash." Alpha 3 said as she pulled the pin off a flash grenade and tossed it into the corridor. It exploded just after hitting the floor, releasing a blinding white light that stunned the enemies that crowded the corridor.

"Now, attack!" the lieutenant commanded. "Saber 11 was quick on both his feet and his trigger finger, as he gunned down all four of the tangos that blocked the way with his 870 shotgun, pumping out the used rounds, as he fired. "Hey! You Bastard, you stole my kills!" Saber 7 shouted. "Well damn… I guess I did. Deal with it." The boy said as he pumped out a spent shell from the jet black weapon. "Damn you, Sheen!"

"Knock it off, you two." Alpha 3 said as she moved down the corridor, carefully avoiding the bodies. She stopped at the end of the hall, in front of a door way, and peeked inside the cargo bay. Inside they were large metal containers, small vehicles, wooden creates, and to top it all off, hostiles armed with AK-47 and AUG A3 assault rifles, MP5 and P90 SMGs, even M60 light machine guns.

'What the hell? This wasn't in the reports I received. Military intelligence, it's always right.' The lieutenant sarcastically thought as she counted the number of tango in the room, noted their positions and carefully thought out plan of attack. "Okay Sabers, listen up. Saber 7," "Ma'am." The young girl replied. "I want you toss a frag right into the center of the room, that's where most of the enemy soldiers are. The rest of the tangos are on the catwalks across the room, Saber 5, I want you to take those bastards out. Got it?" Seven took out a fragmentation grenade from a pocket on the side of her vest, while Saber 5 switched to a G3 assault rifle. "Copy that Ma'am." "Yes, Ma'am"

Saber 7 moved towards the open doorway, pulled the pin, and waited a couple of seconds before tossing the explosive into the center of the room. The enemy agents inside heard it bounce once before it exploded, taking anyone in the blast radius out instantly. "What the…? Sarge! The Captain's dead! Huh? Enemy units! On the catwalks!" a New World agent shouted and pointed to the young agent that stood in the door way.

She raised her gun and fired five rounds at New World private, killing him in a matter of seconds. "It's rude to point you know." Saber 7 said as she ran across the catwalk. "Now, Saber!" Alpha 3 yelled as Saber 5 came charging in, taking the enemy out just as the lieutenant had planned.

The battle last two minutes at best and the soldiers moved down the stairs to the other side of the ship. They continued trough the cargo hold, till Alpha 3 heard a noise, coming from one of the contains. "Sabers, hold up…" She suddenly said. "What is it, Ma'am?" Saber 5 asked. "We're being tailed, aren't we?" Saber 7 spun around and pointed her gun to a trashcan one of the New World agents had placed under the catwalks. "You hear that, you little bastard! I'm on to you!"

"… Ruby… you're yelling at an empty trashcan." Sheen sighed "How do we know it's empty? Huh? What if there's a Ditto morph hiding inside that can? What if it's disguised as a used tissue? Huh?" Ruby said twitching her left eye a bit. "What's wrong with you?" "They say war robs soldiers of their sanity." Saber 5 suddenly said. "Looks like it's finally happened to her, Ruby's lost her mind… and it only took seven months." "What was that, Samuel?"

"Enough! Sabers, we're here to kill the New World, not each other. So, as your superior, I'm kindly ordering you to KNOCK IT OFF!" The lieutenant shouted, as she went to a large orange container and opened the large metal doors. Inside the metal container were creatures that, at a glance, looked like large Pokémon. But upon closer inspection, they had human features, such as paw like hands and human eyes.

They small group of five all looked the agents with fear in their eyes. "Oh no… their back… and they have guns! They're going to shoot us!" A young boy with a single horn on his head, red scales covering his body and a tail lit on fire, shouted. "Calm down, we're not going to shoot you." "Well… then w-what… What do you guys want?" A young man cover from his head to his lightning bolt tipped tail in orange and brown fur asked the lieutenant, who removed her masked, and let her long pink hair fall out. The group was shocked to find out that the person who had opened the door… was a nurse Joy! "My name is Hope Joyous, and I'm the leader of this team of Kantian soldiers. We're here to get you out."

The Creatures looked to confused for a moment. "…What? Who… What are you guys…?" "There's no time Raichu boy." Hope interrupted the young man. "We're got to a mission to finish. Head up the catwalks, trough the hallway, and head up on deck. They're two more soldiers wanting for helicopters up there. Stay with them until they arrive. Got it?" He nodded his orange furred, yellow cheeked head. "Yes Ma'am." He said, as he and the rest of the creatures ran towards the sergeant and corporal waiting on deck.

Lieutenant Joyous sighed and turned on her com. "Sergeant 1 Grade Haze." She said into her com link. "Yes ma'am?" "You have civilian Pokémorphs coming up. They are lead by a young Raichu Morph. Tell Frankie not to shoot them." "Copy that ma'am. By the way, the birds are here, and waiting for us to finish up."

'This excellent. They're here sooner than I expected.' The lieutenant happily thought to herself. "Splendid, get in one of the helicopters the moment the morphs arrive, and tell chopper you and morphs climb in to leave immediately, and tell the other to wait for us. Understood?" Joyous said as she put her mask back on. "Copy that, ma'am."

"Okay, Sabers, listen up! We're almost done here. Just one room check, and home free." She told the agent. "Alright! Let's over with already then, man! I've got a date waiting for me at home!" Sheen Shouted. "A Date? Really? With who?" Ruby asked. "Britney." "BIMBO BRITNEY?! NO F-ING WAY! HAHAHAHAHA!" Ruby rolled on the floor with laughter. Hope couldn't help but smile, while Samuel just watch the girl die of laughter on the floor, clearly not amused.

"She is NOT a bimbo, she just… likes to flirt." "Really? What about time, she was caught doing the whole Omega Team?" Ruby asked as she got up from the floor, recovering from her laughing fit. "Well S-she-" "Don't we have a mission to complete?" Samuel said as he headed to the next room. "Saber 5 right, agents, we have to finish this." Hope said as she caught up with Samuel. "I'll make fun of your slut of date later… but for now, I'm some things to blow up. (evil chuckle)" '…She scares me sometime.' Sheen thought.

The agents entered the next part of the cargo hold, expecting a fight… cut to their surprise it was empty. "What the hell? Where are all the hostiles at?" Sheen asked. "Don't know. Maybe they we were coming, and jumped off the ship." Ruby remarked. "Stay on your toes, agents… they could right around the next corner." Lieutenant Joyous warned.

"Yeah, well I wish they'd come out of hiding and die like bastards they are." Ruby said. "I mean morphing your own agents is one thing… but kidnapping and morphing innocent people that have not to do with this war? That's just unforgivable." Hope sighed as she remembered how Ruby was recruited into the secret part of the Kantian Armed Forces.

The poor young girl's family and friends were to be morphed for unknown reasons… she was the only one to escape. Hope knows the feeling of losing a loved one because of the New World all too well. Ironically she too had lost everything because of the New World's plans. Her friends, her Pokémon, her parents… her brother…

"Ma'am!" Samuel shouted, interrupting her thoughts. "What is it, Private?" "You may want to take a look at this." He said as he opened a black metal container's large doors. Inside was a chamber large enough to fit a person in and two small slots, the size of Poké balls on the sides of the machine.

"Wha… what is that thing?" Ruby asked in shock "It's a New World morphing machine!" Sheen shouted "What? How do you know that, Sheen?" "Because I was put in one of those damn things when the New World captured me. If it wasn't for Saber 4 and Saber 14… the poor bastards. "Now's not the time, Sheen. Let's get that thing ready for transport."

"RAWR!" "…Sheen," Ruby said in a small voice. "Please tell me that was your stomach…" "RAWR!" The team looked around, weapons drawn, as they looked for the source of those unnatural, inhuman screams. Suddenly an extremely large create at end of the room exploded, and a giant unknown creature came out. The beast had three heads that nearly hit the ceiling of the ships hold. The head on the right was that of a Salamence, the head on the left was a Grachomp, and the head in the center was that of a Charizard. It had two long gray scaly tails that were both on fire, a black fin scaled, between two Charizard like wings on its back, and razor sharp claws on its hands and feet… if that's what you want to call them.

"W-WHAT… WHAT IS THAT THING?!" "It's a New World experiment! Ruby look out!" Hope shouted pushing the private out of the way of a triple hyper beam attack. The three energy beams melted three large, gaping holes, the size of a normal person, into the wall "Agents, Gun it down!" Hope ordered. The agents opened fire on the mysterious beast… but unfortunately for the agents, the rounds bounced off the monster. "Damn! That did nothing but piss it off! We are so screwed!" Sheen shouted.

"Calm down, Saber 11! There's got to be a way kill thing. And we're not resting till find it!" Hope shouted. "Besides, it's not like the ship's going to sink or nothing." Ruby said trying to look on the bright side of things.

"Alpha 3, this is command." Hope's com suddenly said. She recognized the voice of a commander she's meet before, however she could not remember the person's name. "Go ahead command." "We've got some upsetting news. Our radar has picked enemy fighters come in fast. ETA two minutes and closing."

"You've gotta be kidding me! What else can go wrong?" "LOOK OUT!!" "WHOA!" Samuel knocked Ruby to the ground and kept her down as a gaint wave of flames flew over them. "Agents, this is Sea Knight 10, we can't hold our position any longer. We are close to bingo fuel. You guys got two minutes at best." The Sea Knight helicopter reported over the com.

"Ya had open your mouth, Ruby! Now we are officially Fu-" "Can it, Saber! We're getting out of here now!" Lieutenant Joyous shouted as she hit the floor barely avoiding another triple hyper beam. "Sabers on my go, we'll toss flash bangs at each one of that things heads, blinding it long enough for an escape!"

The agents readied themselves, "Now!" The agents tossed the flash grenades at the beast heads, and blinded all three of them. "Now! Fall back!" Hope said waving her hand signaling the agents to retreat. "Status report, sergeant!" "Ma'am, as soon as the morphs came on deck, we rushed inside the helicopter with them. We're heading home, and Sea Kni- bloody hell! Lieutenant! Get outta there!"

Once through the melted wall, the agents took only a couple of before being suddenly knocked of their feet by a huge explosion. "God Dammit! What the hell was that?!" Sheen yelled as scrambled to his feet. The room began to fill with water, as the sea gushed trough a hole it the ship. "The ships been hit! We're sinking!" Hope shouted as the team got back on their feet, all except for Ruby, who was struggling to get back to her feet.

"Damn! Ma'am that thing's getting back up!" Samuel shouted. Suddenly another torrent of water burst through the hull wall next to the monster. "We don't have time for this! Hurry up and get on deck." Hope rushed over to Ruby and helped her up. "On your feet, Saber! We're getting out of here NOW!" The agents rushed up the catwalks, and ran back into the corridors, just as the experiment was submerged under water.

"Alpha 3! Are you guys still alive? Come in Dammit! Where the hell are you guys?" The Sea Knight panicked. "Stand by we're on the way." Hope said, showing that the team wasn't dead… not yet at least. They continued running through the sinking ship, falling to their knees with every rumble the sinking ship made, finding it harder and harder to run as the floor stared to tilt. Until finally they were on deck. However the ship was listing heavily to the left and the stern of the ship was completely underwater.

"Where the hell is that damn chopper?!" Sheen yelled as they ran up the now airborne part of the ship. As he said this a Sea Knight transport chopper immediately, flew in front of the dying ship, and the entire team quickly got aboard… all except for a certain young, red headed agent of theirs. Ruby had lagged behind during the escape, and found it hard to run up the slippery bow of the ship.

The ship was going under, the chopper was getting farther away, and Ruby was running out of time… she did the only thing she could do. In a last ditch effort to save herself, Ruby jumped off the bow of ship and grabbed the ramp of the helicopter, hanging over the sea like a fishing lure. However her hand was slipping and she was about to loss not only her grip, but her life as well. "Gotcha!" Hope shouted as she and Samuel grabbed her arm and pulled into the air transport vehicle.

"We're all aboard! Take us home." "Copy that, Lieutenant. Next stop, Viridian City Headquarters." The pilot said as they set a course for home. "You are one very lucky little girl, you know." She said to the Saber that removed her mask, and was hyperventilating on the floor of the helicopter. "And you wonder why people 'Reckless Ruby'." Samuel commented.

END TRANSMISSION

Military intelligence, it never fails. (sarcaism) Anyway that's the beginning, and this only the start. By the way, for those that have noticed, this chapter is based of the first level of Call of Duty 4. Yeah... well I've been playing that a lot lately... so... Love it or hate it, just please review it.