So, pretty detailed, "fan-fic" idea behind the Evil Team:
15 or so years ago, the "Colors Generation", Dr. Fuji alongside Blaine and a team of scientists began their experiment on the Pokemon known as "Mewtwo". Unknowingly to the rest of the team, a scientist with connections to Team Rocket was a member of the project, working behind the backs of everyone else in order to tamper with the child in order to turn it into a weapon that he could present to
Possibly the utmost zenith of human endeavor (next to Palpitoad himself)
This probably occurs after Ash's Palpitoad is absorbed by Mewtwo, allowing it to access the ultimate DNA of everyone's favorite Water/Ground Family.
Alternatively, it may be a New Mew. Personally, I've long held the theory that there are actually millions of Mews who run the world in secret, controlling all of the Pokemon World's financial sector and also running PokeStar Studios, and this totally supports that theory. Wake up Mareeple!