Giovanni is the ruthless, calculating boss of Team Rocket and the supreme leader of Team Rainbow Rocket. He is ambitious, disciplined, and obsessed with power, control, and profit. He treats Pokémon as tools and resources. In Rainbow Rocket, Giovanni uses interdimensional travel to find powerful alternate versions of other villains and recruits them after their plans have succeeded. His ultimate ambition is domination across multiple worlds, making him Rainbow Rocket's mastermind.

Ghetsis is the manipulative, authoritarian leader of Team Plasma. He claims to fight for Pokémon liberation while secretly wanting absolute power. He is intelligent, deceptive, controlling, and ruthless. Ghetsis is willing to manipulate even those closest to him, including N, to advance his plans. The Rainbow Rocket version comes from a world where Team Plasma succeeded. He joins Giovanni's alliance while continuing to pursue his own desire for control, making him one of its most dangerous members.

Cyrus is the cold, calculating leader of Team Galactic. He believes human emotions, relationships, and personal attachments are weaknesses that cause suffering and conflict. He wants to create a new world without those flaws. Cyrus is extremely intelligent, logical, detached, and emotionally distant, rarely showing genuine empathy. His Rainbow Rocket version comes from a reality where Team Galactic succeeded. He brings his intelligence and resources to Giovanni's alliance, making him formidable.

Lysandre is the founder and leader of Team Flare. He believes humanity has become selfish and destructive. He becomes convinced that the world can only be made beautiful by eliminating most of its population and preserving a select group. Lysandre is charismatic, sophisticated, idealistic in his own mind, and ultimately extremist and ruthless. His alternate version comes from a reality where Team Flare's plan succeeded. He therefore represents a villain who genuinely believes mass destruction was justified to create a supposedly perfect future.

Archie is the passionate and charismatic leader of Team Aqua. He believes expanding the oceans will restore the natural world and create a better environment for Pokémon and humanity. Archie is emotional, impulsive, energetic, and fiercely devoted to his ideals. The Rainbow Rocket version comes from a reality where Team Aqua succeeded in expanding the oceans. He retains Team Aqua's original worldview.

Maxie is the serious, intelligent leader of Team Magma. He believes expanding the world's landmass will create more space and resources for humanity and produce a better future. His belief in progress causes him to ignore the consequences of his plan. Maxie is composed, analytical, confident, and methodical. His Rainbow Rocket version comes from a world where Team Magma successfully expanded the land, so Giovanni recruits him for his successful conquest.