So I had this idea a while back, and I just had to write it. Basically, this is an AU where a Dark Arceus beat the real one 100 years before the storyand took over the entire Pokemon world. The main characters of the Pokemon series like Ash, or Misty, are all 20, so they don't remember the world before the takeover.

Ash Ketchum

20 year-old Ash Ketchum, a simple foot soldier from the Kanto branch of Team Cosmos, sat in camp with his squad. They, along with hundreds of soldiers from all the regions, had been re-deployed to Unova, to quell a group of rebels that had been attacking patrols and supply lines across the region. He grinned as his two best friends, Brock and Misty, returned from patrol.

"Hey. Anything out there?" he questioned, fingers drumming nervously on his rifle. His Ekans hissed as it slithered up next to him. Misty sat down on one of the camping chairs with a huff.

"Nope. Houndour didn't smell anything, and we got nothing on infrared either. If the rebels are out there, they've got some serious stealth abilities."

"Yeah." Brock chimed in. "Not even a gunshot or a rebel Pokemon to be seen."

"Cool! I've got first watch tonight, should be easy if the rebels are all hiding."

"Hey Ash, where did the other three go?"

"Sleeping. They have dawn patrol."

"Alright."

The three quickly cooked their dinner, and Ash settled in by the fire to keep watch, while Misty and Brock ducked into their tents. Nothing stirred, and he sighed, resigning himself to six hours of boredom.

Shade Ceo

Shade moved silently through the darkness of the forest, his black trenchcoat and armor hiding him in the darkness. His sword was heavy on his back, and his twin revolvers were holstered under the coat, as his sides. His kukuri fit perfectly in his hand, and he raised the curved knife as he pushed through the undergrowth to the enemy camp up ahead. His Gengar, Scaith sat on his shoulder, and he could hear two other rebels, Drayden and Cilan behind him. The three stopped just outside of the camp, at Shade's signal.

"Cilan. Clear those three tents, kill the occupants quietly. Drayden, cover me, I'm going for the sentry. The other two should be out on the midnight patrol, Gengar, go look for them."

The other two nodded, and white Cilan slipped away behind the three tents, Shade broke cover and moved up behind the sentry. But everything went wrong.

"Ash?" a voice called from behind him. "Shit! You! In the black! On your knees!" A redheaded girl had come out of the tent behind him, the ones that should have been empty, and had a rifle pointed at his head. The sentry grabbed him from behind and pinned his arms to his sides.

Suddenly, a shot rang out and the girl dropped to the ground, holding her leg. Shade brought up his leg, slamming his boot into the sentry's crotch, and spun, knocking him out with a brutal punch. A man with dark, spiky hair, rushed out of the tent, only to be tackled by Cilan and knocked out. Shade grinned and dusted off his coat, his Gengar re-appearing from the forest.

"Gengar!"

"Yeah, I'm fine pal. Don't worry about me."

"Gar."

"Yeah. I know I should have checked the other tents."

"Gen. Gar!"

"I get it!"

The young man grinned, nudging the unconscious sentry with his toe.

"Grab these three, maybe they can tell us more about the enemy's new forces."

Drayden hefted the man with the spiky hair over his shoulder, and Cilan scooped up the enemy sentry, leaving Shade to carry the redhead. The rebels, along with their new prisoners, disappeared into the night.

Misty Kasumi

Misty woke up in a small cell, on a small cot. Through the front wall, made out of steel bars, she could see Ash and Brock in a similar cell, though theirs held two beds. She groaned, standing up, and collapsed to the floor as she put weight on her injured leg.

'Shit!' she thought. 'Forgot I got shot…'

Ash and Brock had heard her cry of pain, and she heard Ash call out.

"You alright Misty?"

"Yeah! Leg hurts. Any idea where we are?"

A new voice interrupted from just down the hall.

"I can answer that for you. You're in the prison of An Caisleán, or the Castle, headquarters of the Followers."

"The Followers?"

"You might call us the rebels. In actuality, we're an ancient sect of warriors that worship the old gods, like Arceus and the Legendaries. We were here before Team Cosmos and their Chenborog bullshit, and we'll be here long after Team Cosmos falls. Chenborog may be real, but he's no god, not like Arceus."

Brock shouted out in anger,

"Chenborog is the true god you heretic! You'll pay for this!"

"Sure. Whatever. But for now, we're busy. Your boss played right into my hands, moving troops out of Sinnoh to fight here, when my real target is there. In a few days, the first part of the Prophecy of Arceus will be fulfilled, and Chenborog's days will be numbered. Arceus will return, to fight the darkness of his foe, and Cheborog will fall to the light, freeing us once again."

"The fuck does that mean?" Misty asked.

"Chenborog was born at the same time as Arceus, the dark to Arceus' light, evil to Arceus' good. The prophecy of Arceus tells that Chenborog wants only to rule the world, to have everything under his oppressive control, and that once he does, heroes will rise up, find his children, and bring him down from the heavens to fight Chenborog."

"So what. The legendaries were defeated by Chenborog the first time, he'll beat Arceus and the other Legendaries again." Brock shouted.

"Perhaps. But the fact remains, things under Chenborog's rule are bad. People and Pokemon, dying of disease, starvation, and worse. Anyone who doesn't conform, disappears. Even if Arceus loses, I fight for a free world, where children don't go to war at age ten, where people have enough food and medicine to go around. A world of good. Not the dark of Chenborog."

"Chenborog is a kind and benevolent lord. He provides for the true believers." Misty muttered. The Follower seemed to be losing his patience, and he finally broke.

"You continue to repeat the lies you were taught! Chenborog thrives on misery, he causes the diseases and famine to keep control! Eventually, he WILL consume everything, and you're too blind to see it! Join us! Do the right thing!"

The three stared at him.

"Fine." The man turned, stalking off.

Shade Ceo

'Damn idiots.' Shade though as he moved up into the light of the courtyard. Around him was the citadel of An Caisleán, the home of the Followers. Soldiers and their Pokemon patrolled the walls. The city was home to almost twenty thousand people, some, born into the Followers, others normal people who had stumbled across ancient copies of the prophecy, and some just refugees, looking for a life outside of Chenborog's tyrannical rule. It was a haven, beautiful and strong. But Shade knew that the gathering storm would soon engulf the last safe place in war.

Despite this, he grinned as he exited the prison courtyard. Suddenly, a massive creature was in his path. A long, serpentine body of black and red, long tentacles of shadow, and a huge head with jaws open. Giratina, the Renegade stood before him.

"My friend. You go to appeal to the council?"

"Yeah. If they give me permission to go to Sinnoh and find the Warrior Weapons, the prophecy will begin, and this war will end. Can you imagine that?"

"I have no need. I was there when Arceus fell, when the darkness consumed our world. I was there before that too."

"We can do this."

"Yes. We can."

"No"

"But why?"

"You are needed here Ceannaire Ceo. We have no time to spend chasing a myth that may give us a slight advantage, when we can win here with concentrated efforts."

"But we can't! We're fighting a losing war here!" Shade shouted in disbelief.

"No. You will not go to Sinnoh, you will focus on trying to turn our new prisoners. Allow them to befriend Pokemon that wander in. Once they come to love Pokemon, instead of seeing them as tools, show them the city, get them to join us."

"Yes Elder."

Shade left the council room in defeat.

"Denied. This is BULLSHIT!" he shouted, slamming his sword into a tree.

"Agreed. As much as I believe we should just go anyway, it would not serve our interests at this time. We need to get the new prisoners to work with us first."

"Yeah."

I used a lot of stuff that isn't English in here for the Followers, translations below.

Ceannaire: Chief/Leader

An Caisleán: Literally, The Castle

Ceo: Mist