Here's an idea that I've got pretty well developed. If I had any skills, I'd probably be looking to put together a team and actually make this hack. You begin as a lab assistant in Prof. Pine's lab. You awake one morning to see an excited e-mail about a pair of fossils and an opportunity to bring them back to life. When you arrive it lab, it's disheveled as usual - Prof. Pine was never very organized. A holorecording then activates, and it's Prof. Pine explaining that he was called away suddenly, and unfortunately one of the fossils proved to be fake. But you can revive the other one and please do some field work, battling with it and learning about its behaviors and capabilities. It's a dome fossil, and you get a Kabuto. As time goes on, you're contacted by Prof. Pine a few more times, and he gradually becomes more and more suspicious, until it becomes apparent that he's being held captive and making these recordings under duress. Meanwhile, you encounter Team Rocket or Team Helix (not sure if I'd prefer to use the standard bad guys or name my own team). Their goal is world domination, and toward that end they're working at engineering new, more powerful Pokemon. Team Helix uses some "Fakemon," and even their real Pokemon are often hacked to have illegal movesets. Like a Magikarp with Hydro Cannon, Blast Burn, Frenzy Plant, and Hyper Beam. (Hypothetical example). You'll probably encounter a Venustoise. Other fan theories are made canon - Voltorb really are failed experiments into early Pokeballs, possessed by Haunters/the ghosts of Pokemon that were captured and can't escape. Gengar really is Clefable's shadow. Ditto really are failed attempts at making Mewtwo. Genesect really is a Kabutops in armor. Eventually you do rescue Prof. Pine, and you find that Team Helix has made Mewtwo (from the stolen Mew fossil, which was the other one Prof. Pine had). The Mewtwo goes berserk and the world seems to be in grave danger. Prof. Pine comes up with a plan - they were also working on plans for a Genesect, and that may be the only thing powerful enough to face Mewtwo. That's why they were using the character to begin with - a dupe to train the Kabuto for them in order to get Kabutops. Prof. Pine is leery of the idea, but the bond you have with your starter may be enough to ensure Genesect doesn't go similarly unruly. In other words, Kabutops evolves into Genesect by an event that requires high happiness. I'd also like to put a Deoxys in that keeps running and changing forms. It may be implied by programming in three running legendaries (speed, defense, and attack formes) that only start appearing after you encounter a normal form Deoxys that runs. Mind you, having three kind of makes it difficult to believe. I wonder if there could be a way to hack the Castform sprite change and just use a single running legendary? Form change might end up becoming weather dependent, but oh well. Also, one of the Gym Leaders has a Porygon2 that gets upgraded to a Porygon-Z but gets a virus and goes berserk. So there's a retrieval mission that just happens to also make wild Porygon family members appear in the wild during this time. Essentially, the virus is duplicating itself.