Game-verse Fiction Idea!: This is something I'll be thinking about while I work on a different, non-Pokemon related piece of work.
A channeler-turned-mercenary, Grajakal, (town of origin being Ecruteak) sees the landscape of the world changing; he sees he plots being enacted by Teams Aqua, Magma, Galactic, Plasma, and sees a future of nothing but war if the Teams are not stopped. They would become their own Superpowers. Thus the mercenary decides to join Team Rocket; they are unburdened by the morals upheld by the leaders of the other Teams. The other Teams pretend to adhere to a moral code to justify their desire to awaken and control exceedingly powerful Pokemon.
The mercenary Grajakal joins Team Rocket and decides to work with them creating "dark pokemon." These "dark pokemon" would be similar to those from the Team Rocket expansion set (WOTC Tcg) with "Dark" in the Pokemon's name. The mercenary intends to use his training as a channeler to allow his pokemon to control the "Dark" nature implanted in them by Team Rocket. I haven't quite figured out just what makes Pokemon "Dark." I think that "Dark" will be a reference to the earliest pokemon. Before humans began forming relationships with them and using Pokeballs, Pokemon were wild and primal. Since the first Pokeballs were able to curb these wild, primal, elemental tendencies. Thus when these first captured Pokemon were bred, humans began breeding the wild, primal, elemental tendencies out of them.
In the present of my fiction, not even wild Pokemon exhibit the level of ferocity and viciousness of "Dark" pokemon. Given that the viciousness characteristic of "Dark" pokemon harkens back to their origins, I'd say Team Rocket uses some kind of genetic manipulation to switch on the alleles that instill those survival mechanisms in the Pokemon.
While Grajakal is driven to work his way into the upper echelons of Team Rocket. The mercenary-protagonist hopes to use his influence to sent Rocket agents to the other regions--Hoenn, Sinnoh and distant Unova--in order to interfere with the plans of the other Teams and improve the science behind awakening those primal genes within pokemon that turn them into what the media dub "Dark" pokemon. The mercenary-protagonist's plans unwittingly reawaken the entity Missingno.
Missingno is a pokemon compose of raw elemental essence with an Id, Ego, and Superego. The glitch pokemon it creates will manifest as Id-driven mutations. Missingno wants to return the world to a state of unformed matter from which it can create a new world. The mercenary-protagonist returns to Ecruteak to learn as much as possible about Missingno. He still wants to try to use Missingno as a glass-canon against Team Plasma.
Meanwhile Channelers throught the Pokemon World are called to deal more hostile encounters between Ghost-type Pokemon and humans. One of the Channelers, Jannik, decides to look into academic literature concerning Ghost-types. Many Channelers discount the studies on Ghost-types published by Morty, Agatha, and other well-known Ghost-type trainers; these Channelers believe that these one-time Channelers used the art of Channeling for their own gains. Jannik learns that Ghost-types are dimensional librarians; they catalogue the events in the world they witness before the world's ending and remaking.
Jannik's travels range from Mt. Pyre, to the Old Chateau, to any haunted regions in Unova (haven't played B2/W2 yet; need to for research). Jannik sees the results of Grajakal's war against the other Teams. It appalls her until she's captured by one of the Teams durin her travels.
Grajakal meanwhile is working at exploring the connection between the "Dark" pokemon and Missingno while overseeing his clandestine war against the Teams. Missingno is an entity that feeds off the elemental essence imbued within pokemon from the point of their creation. This elemental essence grants them their typings, abilities, and attacks. Grajakal comes upon the aftermath of a battle. It shocks Grajakal; his war agains the Teams never involved anything as openly destructive as this. Some of the Rocket's scientists are among the casualties. The culprits are a rogue band of Channelers who believe that the Pokemon League are working with Team Rocket to kill them and take their children away for scientific study.
Grajakal has further encounters with this rogue band of Channelers, and meets up with Janik during one encounter withthe rogue Channelers. Grajakal and Janik discover that the Ghost Marowak is controlling the leader of the rogue Channelers. The mother Marowak wants to distract Grajakal from finding a way to use Missingno because when Missingno reverts the world to unformed matter, she will get to be with her baby that was killed by Team Rocket. The mother Marowak takes vicious glee in destroying families via the rogue Channelers in her crusade against Team Rocket.
Grajakal and Janik learn that Missingno is drawn to the alleles in the "Dark" pokemon that augment their attacks and temperament. Thus Grajakal and Janik devise a plan to unload the strongest of their "Dark" pokemon en-masse in Unova, at Team Plasma's Head Quarters. Grajakal and Janik decide to use the submarines Team Rocket has captured from Team Aqua as well as the ships the Team owns at Slateport. Glitch Pokemon serving Missingno attack the ships and submarine, destroying the fleet and the sub.
Grajakal and Janik are forced to flee the Glitch Pokemon; they use the Glitch Pokemon to shake off the Rockets Giovanni sent to bring in Grajakal (as he is getting suspicious of Grajakal's hand in the current events). Janik talks Grajakal into abandoning his idea of using Missingno against Team Plasma. Janik tells Grajakal what she learned from the Ghost-type pokemon: Missingno came into being in the unformed stuff of creation that eventually became Kanto. Kanto is an older region of possibilities and memories; thus it will take the Elemental Six of Kanto to bring Missingno down: Blastoise, Charizard, Venusaur, Alakazam, Gengar, and Chansey. These are Ancient Pokemon predating the Legendary Bird Trio.
In Kanto the Bird Trio are under the control of the rogue Channelers and are being used to hunt down Grajakal and Janik. After besting the Legendary Bird Trio and awakening the Elemental Lords, Missingno is imprisoned within the depths of the Unknown Dungeon and guarded by the Elemental Six. Janik leaves Grajakal to deal with the rogue Channelers while Grajakal goes on to use the chaos to his advantage by proclaiming that Giovanni was killed by the Glitch Pokemon and Missingno. With his army of Rockets and "Dark" pokemon, Grajakal goes on to continue his war against the Teams that're trying to awaken their regions' respective uber-Legendaries.
END
