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Go full neon genesis on it.
Obscure symbology
Sleeper Pokemon/human hybrids
All the team rocket variants subtlety or not so subtlety advancing their separate plots, shadowy conflicts between crime teams.
The main character is the leader of an elite mercenary squad, on the payroll of all six teams, sometimes called in to mediate on interteam conflicts, more often to retrieve rare artifacts, tech, and Pokemon.
As each team's plan nears completion, the main character starts piecing together how insane they truly are.
The ending episodes go like this: recruits Mewtwo, jams radio signals, face down the space and time legends.
Tracks down Rayquaza, Ranger squadmate performs an epic capture, makes kyuogre and groudon settle down.
Sabotages team flare's crazy canon, accidentally releases Ybird, capture it through sheer grit and manliness.
N does a worldwide broadcast, all three unova dragons backing up the plasma agenda. There is a tournament to see who will face N and prove him wrong, composed of each region's league champion and the main character gets in on strength of reputation and connections.
Wins, faces N in climactic battle, almost loses, but Mewtwo pulls a Hannibal lecture on the remaining Pokemon, Zoroark, who allows Mewtwo to knock it out.
Ghetsis freaks, has a sixway battle with the rest of the mercenary squad, loses. El pollo diablo, held in reserve, mind breaks him, Ghetsis is now hollow husk of a man.
Mercenary squad are heroes, retire to pursue hopes, dreams, and lap of luxury. Main character becomes a highly paid interpol peacekeeper, with penthouses reserved in every major city.