Few villains are as iconic as Pokémon's Jessie, James and Meowth. Team Rocket is beloved by fans of all ages as the lovable goofballs who pursue Ash and his Pikachu across the entire Pokémon world, often finding themselves soaring into space as a result of their schemes. Despite their goofy demeanor, however, Team Rocket can accomplish great things when they apply themselves, as seen in the Alola Region when Jessie and James placed fairly high in the Manalo Conference.
However, when going back to the early episodes of Pokémon, Jessie and James seem almost unrecognizable when compared to later seasons. The first 12 or so episodes of Pokémon, right before the team reach Cerulean City, feel like a far more competent, intimidating threat. This has led some fans to speculate that maybe Jessie and James were cloned.
The Team Rocket Clone Fan Theory
On the Fan Theories subreddit, one user recently posted a theory speculating that Team Rocket was cloned. The user speculates that the Team Rocket who appeared at the start of the series was simply too competent to be the same characters who, only a few episodes later, would end up trapped on the SS Anne and unaware that Magikarp was a somewhat useless Pokémon.
The theory argues that Giovanni already had access to cloning technology, thanks to the Mewtwo project, which, at that time, was ongoing. Every time Team Rocket was blasted off into space, they'd burn up on re-entry or die, which would result in a new Team Rocket team being sent out, each with the memories of the original. To this end, Giovanni also wants them to capture Pikachu because Pikachu can be used to power up the cloning devices. This makes Pikachu a high-priority case for Giovanni.
There Are a Lot of Holes in This Pokémon Theory
Though it's a fun thing to consider, this theory has a lot of problems. For one, Team Rocket and the others remember their prior exploits. If all of them were clones, they would be unable to remember any of their previous experiences. Not to mention, Team Rocket is often shown pulling themselves together after being blasted off, indicating that they definitely survived each blasting off point.
Furthermore, Team Rocket isn't always incompetent in later episodes; at times, they're still highly capable thieves. They consistently demonstrate engineering skills with various machines and devices used to capture Pikachu. During Pokémon the Movie: 2000, they even use their skills to help Ash save the world. During the Alola League, they prove they're incredibly competitive players when Jessie ranked in the Top 16 and James ranked in the Top 8 out of over 151 of the strongest trainers in Alola.
Giovanni Couldn't Clone Team Rocket Even If He Wanted To
The biggest hole in the theory, however, is that Mewtwo was the first and only specimen to survive Giovanni and Dr. Fuji's cloning process. When Fuji tried to clone his dead daughter Amber in "The Birth of Mewtwo," AmberTwo, along with multiple other cloned starters, all die. Mewtwo is the only success Giovanni had at cloning. Mewtwo later destroyed all the cloning technology, only to rebuild it for his own purposes. Giovanni never had access to this rebuild technology nor knew of its existence, and it's unlikely it even existed after the events of the first movie.
Not only would it make little sense for Team Rocket to be cloned, but any aspect of this theory that tied into Giovanni's cloning technology falls apart when you realize that Giovanni had nothing to clone Team Rocket with. Mewtwo was a fluke for Giovanni, which was why he couldn't just make a new Mewtwo when Mewtwo ran away.
Ultimately, the fan theory, while interesting, simply cannot hold up under scrutiny. The Team Rocket who won in the Manalo Conference is the same Team Rocket as there always was.