They Gave No Quarter

Why is it Deoxys, Mewtwo, Darkrai, and Genesect are made out to be bad guys?
Simple answer, they couldn't be controlled. They had raw, untamed power that Arceus feared, so he branded them as evil beings, creatures that needed to be slaughtered. To ensure their own survival, they banded together.
Samuel- The Genesect and the most intelligent.
Marcus- The Darkrai and the most foreboding and dark.
Roland- The Deoxys and the most playfu; and fun.
Caro- The Mewtwo and the wisest and gentlest.

The were the Outcasts, so they said.
For many years, there was peace between Arceus and the four he had banished. Untill one day....

Ch.1: Grave News
Vincent the Raikou was anxious. He hated delivering Arceus bad news, especially during the celebration of Giratina's return from exile. He thought his name was Cephor or something creepy like that...

Zane the Victini was on guard at the gate of the Hall of Origin. He saw Vincent and immediately opened the gate with a quick salute.

Vincent didn't acknowledge the sentry, for he was far too busy. Trying not to run but still trying to get there as fast as possible, he stumbled over himself several times. Many took notice of his nervousness as he passed by.

Vincent's brother Garth the Entei looked at him sternyl as he passed by in a mad, jumbled rush, but said nothing to his troubled sibling.
Finally, exhausted but triumphant, he arrived at Arceus' throne room.

"M'lord!" he cried in horror, "Dialga is dead!"

Arceus looked at him sharply, "Are you sure?"

Vincent nodded. He cowered beneath the advancing shadow of Arceus.
Cephor floated in, "Gaia try not to hurt him too much now.... you'll stain the floor."

Gaia gazed at his brother, "Why must you taunt me? Are you not grateful for me freeing you from your imprisonment?"

"You freed me 1000 years late brother." Cephor said coldly, turning away from him.

"Don't turn your back on me!" Gaia thundered.

"Perhaps you shouldn't turn your back on me..." he replied ominously.

"Is that a challenge?!"

"Temper.... I wouldn't dream of fighting you. Because as far as brains are concerned I got the bulk, but when it comes to brute strength I'm at the shallow end of the pool." Cephor said threateningly, "You of all people should understand this. After all, we're twins, why wouldn't you know this?"

Gaia lowered his voice, "Fine, but please calm you wrath for another day my dear brother, for it appears Dialga is dead."

Cephor spluttered, "WHAT?! Who hath dared to do such a thing?! They shall be torn apart slowly, and painfully and then they will regret ever existing in the first place!!"

Vincent was stuck to the wall, terrified, "It seems to was Marcus and Roland M'lords...."

Cephor's eyes narrowed, "The outcasts... they will die."

Very nice story I like it

Roland and Samuel sat quietly in Cerulean Cave, silently thanking Caro for bringing them here for the peace they so desired. Now while what they truly wanted was to get back to the Council and Arceus, they knew he hated them, so they stayed away at all costs, not wanting more hassle from the self-proclaimed diety.

They sighed simultaneously, and let out a hollow chuckle afterwards.
Roland stood up. He was in attack form, and his tentacle arms twitched at his sides as he languidly stretched. Suddenly someone unexpected entered. There was Marcus, looking, as usual, brooding and withdrawn. The others felt great pity for him, but never said anything because of how angry he got when they did.

He floated towards Roland, hugged his comrade in arms, the relaxed against the cave wall to sleep.
Samuel gazed robotically over to the left, where Caro was still resing peacefully.
Marcus shook Samuel's claw briefly before falling asleep.

"Roland..." Samuel said oddly, "Do you suppose we should talk to Arceus about coming back?"

He shook his head fervently, "No, he'll just kill us the second we go near him."

Gaia (Arceus) strutted across his Throne Room with an air of indecision surrounding him.
"Should we attack them?" he asked Cephor, "We have no proof, and if we did, they could easily kill our best allies... They are so powerful as it is."

Cephor rolled his eyes at his fraternal twin, "You'll have to wait for conclusive evidence you numskull. Did mother teach you nothing?"

Gaia flinched at the mention of their mother, "Don't speak of her now..."

"Why not?" he asked darkly, "Has guilt taken its toll?"