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Enemy Teams and Organizations
An organisation dedicated to the creation and use of Shadow Pokémon for their own deeds.
- Would Hurt a Child: When they kidnap a baby Lugia to experiment on, they definitely qualify.
A villainous cult that worships Groudon, and is devoted to creating more land for people and Pokémon to live. Led by Maxie.
- Cult: Explicitly described as such.
A villainous cult that worships Kyogre, and is devoted to creating more oceans for Pokémon to live. Led by Archie.
A dangerous organization that desires to create a new universe by controlling Dialga and Palkia. Their leader, Cyrus, succeeded in the previous timeline and destroyed the universe in the process, causing Arceus to throw Ash back in time to try and stop him.
- Big Bad: Of the entire story thus far, as it was Cyrus's plan succeeding in the previous timeline that kicked off the entire plot.
- Hijacked by Ganon: Turns out the Team Galactic of the new timeline were secretly being assisted by the Team Galactic of the original timeline, who planned to use their counterparts' portal to enter the new timeline and take it over.
- Ironic Hell: Their final fate for perpetrating everything is being sent to the "world without spirit" Cyrus wished for... But there is no aura, magic, or psychic powers on their side, no Pokémon, animal wildlife or civilization. And the Pokemon that would go along with them would have their capabilities nerfed, so escaping that same universe is impossible.
- Knight of Cerebus: As the Big Bad, their presence makes any situation more dire. Especially when they use Shadow Pokémon, and especially a Shadow Lucario.
- Perception Filter: For some odd reason, no one can actually see, hear or perceive any action made by a Team Galactic agent, even if it is occuring right before their eyes, and even if they are told of their presence, they quickly forget it. Only characters that Ash has Reminded of the previous timeline are immune.
- The Battle Finale of Legend reveals that Original Timeline's Team Galactic used their own Lake trio to make everyone unaware of Team Galactic in the first place.
- Would Hurt a Child: Fired a gun at Ash (who is still only 14/15), and if not for Absol and Mewtwo, Ash would've lost another life.
An organization that seeks to liberate Pokémon from the cruelties of humans and Poke-ball slavery, led by their leader Ghestis and his son and their King, N.
- Enemy Civil War: Has suffered a schism with N's departure, with two of the Seven Sages defecting with the agents loyal to N.
- For Want of a Nail: With N reading a book about a Pokémon's perspective, he's decided to figure out the real truth of the world and decides to leave to find it, completely derailing the organization's Evil Plan.
The Phantom Pirates
A pirate crew dedicated to capturing the Prince of the Sea, Manaphy, and using him to find the Temple of the Sea. Led by Captain Phantom.
- Arc Villain: Pursued Ash and Co. throughout the majority of the Battle Frontier arc.
- Screw This, I'm Outta Here!: A good chunk of their agents defect after getting on the wrong end of Ash and co.
- Even Captain Phantom's Chatot partner, Casey defects.
- Taught by Experience: Their tactics get more comprehensive the more times they try to abduct Manaphy, though they all inevitably fail.
A mercenary poacher that hunts and captures Pokémon for her clients.
- Combat Pragmatist: Is not above dirty tactics like going for opposing Trainers, or if need be, using actual firearms.
- Knight of Cerebus: When she shows up, things take a much harsher tone.
- It's gotten to the point that some characters get paranoid whenever they see an unexpected Salamence, and have to check if she is still in jail.
- Related in the Adaptation: In this story, she is the sister of Lawrence III.
- Sequence Breaking: Was taken down and arrested during the Orange Islands, three regions before she even showed up in canon.
- Taken for Granite: Has petrification technology in her gauntlet that turns any target Pokémon into a statue.
A collector with a liking for Legendary Pokémon. Is the Big Bad of the Power of One movie.
- Cool Airship: The Kikoku.
- Rich in Dollars, Poor in Sense: As rich as he is, it's amazing how much he goes through trying to rationalize and twist the prophecy to work for him, from touching the orbs to the Legendary Birds, to trying to merge the orbs together, to whispering to them.
- Related in the Adaptation: In this story, he is the brother of Hunter J.
A scientist researching realistic Pokémon simulations and created the Mirage System in aid of that. However, after being ridiculed by the press, he swore he'd prove his genius, by any means necessary.
- Genghis Gambit: In a bid for fame, he created the Mirage Master to assault other places and steal their data to improve his Mirage System, and then planned to defeat it himself to cement his status as a brilliant hero.
- Mad Scientist: Absolutely.
- They Called Me Mad!: Was ridiculed after he presented his first Mirage System only for it to refuse to fight. Then again, he did show it to the press instead of the scientific community first...
A shady businessman who has set up shop in Crown City.
- Early-Bird Cameo: Has shown up a few times before his arc rolls around.
An inventor who had created a machine to siphon away Giratina's power and use it to take over the Reverse World, much to the consternation of his old mentor. Is the Big Bad of the Gracidea Vale movie.
- Artificial Intelligence: Has an AI partner named Infi that assists him in piloting both the Megarig and the Mecha Giratina.
- Ax-Crazy: His flip-flopping rationale on either protecting the Reverse World or not caring if it gets damages are signs that he's not all there.
- Cool Airship: Both the Megarig and the Mecha Giratina count.
- Villainous Valor: If there's any saving grace about him, it's that he cares for Infi as a person and not a piece of technology.
A priest in the past of Michina's town who sought to defy Arceus and keep the Jewel of Life made out of Arceus's plates for the sake of keeping Michina healthy. Is the Big Bad of the Jewel of Life movie.
- Butterfly of Doom: The butterfly in question. Him leaving Michina still unswayed from his beliefs eventually had ripple effects to the future that results in epic catastrophe. Only when Ash manages to save his life and convince him of his errors that the timeline is set right.
- Mind-Control Device: Used suppressing armor on his Pokémon army to keep them from questioning his orders. Only when the armor is removed do they question Marcus's motivation.
- Screw This, I'm Outta Here!: When he was beaten by Ash and co. by force, he decided to leave Michina instead of being vindicated by history. This has unforeseen consequences.
- Well-Intentioned Extremist: Believed that if the Jewel of Life was removed, the land Michina would return to its barren, desolate state, so conspired to keep it by any means necessary, even it meant supplanting his friend Damos and defying Arceus Himself.