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Ho-oh
See Ash's Pokémon
Shaymin
A species from Sinnoh, one of them agreed to come with Ash back to Kanto and clean up the heavily polluted Gringey City. During the Battle Frontier Arc, she moves to Pallet Town, along with the Gracidea flower that lets her form-change.
- Tautological Templar: The Shaymin from Giratina and the Sky Warrior believes that everybody there should believe that Giratina is bad just because they say so. Mawile points out that, while Giratina might be dangerous, dangerous and bad are two different things, and that telling the people saving you off just because you want them to see you as right isn't nice.
Mewtwo
See Ash's Pokémon
Mew
The Mew who fought Mewtwo in the first movie. Has reappeared several times since.
- Ambiguous Gender: Finds binary gender boring, so he/she responds to both male and female gender pronouns.
- Attention Deficit... Ooh, Shiny!: Very much so.
- Badass Adorable: Held his/her own against Mewtwo.
- Beware the Silly Ones: Is normally a complete goofball with no attention span. When he/she actually takes things seriously, Mewtwo gets a workout.
- Psychic Teleportation: Uses this to go wherever he/she wants.
- Time Travel: Can do this by Transforming into a Celebi, though a real Celebi showed up to stop him/her.
Darkrai
A species of Pokémon from Sinnoh and the former God of Death prior to Yveltal's creation. One first appears to Ash when he temporarily dies during the fight with Mewtwo, but tells Ash that he's not going to stay dead because of the Sacred Ash he carries.
- Psychopomp: His duty when death doesn't go... quite as expected.
Lugia (from Pokémon 2000)
See Ash's Pokémon
Silver's Mother
Another Lugia that traverses the Johto region, captured by Cipher for the XD001 experiment. Is the mate of the Shamouti Lugia.
- Bad Powers, Good People: After being un-Shadowed, she still has Shadow Blast, apparently as a means of purging any residual Shadow energy.
- Brainwashed and Crazy: Very temporarily.
- Determinator: She kept firing Shadow Blast to full effect during the Delta Episode after others started weakening.
- Evil Is Not a Toy: Dr. Namba and Cipher tried to enhance the Shadowification process with an ancient artifact. The result was a completely out-of-control Shadow Lugia.
- "I Know You're in There Somewhere" Fight: Had this on the outside with her mate, and then a Battle in the Center of the Mind with Ash's Aura Purge.
Silver
The son of the above two.
- Bratty Half-Pint: Not normally, but if his parents need the Shamouti Birds distracted? They will be distracted.
- No Sense of Direction: When looking for the Temple of the Sea, he somehow went up a river without noticing.
- Wise Beyond His Years: Much better behaved than the Shamouti Bird trio.
The Shamouti Bird Trio (Zapdos, Articuno, Moltres)
The three birds from the Pokémon 2000 movie. Lugia has to keep them in line.
- Badly Battered Babysitter: To Silver, at Lugia's request
- Go Mad from the Isolation: At one point it is suggested that part of the reason for their behavior is the fact that they're mostly alone on their islands.
- It's All About Me: All three want to take over the islands, regardless of the catastrophe that would result, or if they have bigger problems.
- Manchild: All of them are remarkably immature. Lampshaded when Lugia remarks that even Silver is better behaved than them.
The Original Johto Beast Trio (Raikou, Entei and Suicine)
See Ash's Pokémon
The Greenfield/Shiny Johto Beast Trio (Raikou, Entei and Suicine)
The Beast Trio created by the Unown and Molly Hale to fight Ash and co., made real by Mewtwo.
- Become a Real Boy: Thanks to Mewtwo.
- Mundane Utility: The Entei avoids flossing by incinerating anything that can't stand volcanic heat in his mouth.
- Our Monsters Are Different: Were created to fill the roles of a Nuclear Family, as opposed to being resurrected as siblings like most Beast Trios.
- Poor Communication Kills: Planned to visit Molly when she was away, but didn't talk about it with each other, so they all visited at once. Raikou, who arrived last, ended up skidding into a lake.
- Spared by the Adaptation: Entei vanishes along with the Unown in canon. Raikou and Suicine never existed there.
- Suicune was created to replace Delia, who stayed away on a tip-off from Ash. Raikou was just added into the picture to complete the trio, by serving as Molly's brother.
- Unskilled, but Strong: Are every bit as powerful (if not more) as the original Beast Trio, but have no combat experience. This lets the originals mop the floor with them.
- Walking Spoiler: Even mentioning that this Raikou and Suicine EXIST spoils the climax of the Third Movie Arc.
Swords of Justice (Cobalion, Terrakion, Virizion, Keldeo)
A group of Legendary Pokémon from Unova, who set out to Johto in search of Mewtwo. Keldeo eventually joins Ash Ketchum, though he returns to his comrades midway through Hoenn. Since then, they've kept up their mission of protecting others.
Celebi
The Guardian of Forests. Various Celebi appearances may or may not be the same individual, even when they are on-screen together.
- Medium Awareness: They use a book copy of Ashes Of The Past to keep track of what they need to change. They also mention that they need to keep it wherever it originated from to prevent the author from being irked at spoilers for things they haven't written yet.
- Mundane Utility: Celebi uses time travel to go into the future, and retrieve a sequel book, which hasn't been written yet, to one she just finished reading so she won't have to wait for it.
- Time Police: Are tasked to making sure the timelines progress as normal, especially after Time Crashes. One notably invokes this on Ritchie.
- Time-Travel Tense Trouble: Gives this to everyone.
Latios and Latias
See Ash's Pokémon for the main pair. A species of legendary Dragon/Psychic Pokémon, some of whom serve as the guardians of the city of Alto Mare. Another Latias belongs to a Nurse Joy who's part of the Pokémon Inspection Agency, a group which inspects and grades Pokémon Gyms and has the authority to shut them down if they don't meet the standards. This Latias is currently dating Ash's Latios.
Jirachi
See Max's Pokémon
Deoxys (Purple and Green)
The extraterrestrial Pokémon from Pokémon: Destiny Deoxys, befriended by Tory Lund from LaRousse City.
- Reading the Stage Directions Out Loud: This is what their telepathy sounds like, providing sensations and feelings rather than actual words.
Kyogre
Legendary Pokémon of Hoenn whose existence dates back to the beginning of time. She created the oceans, summons harsh rain with her presence alone, and has an eternal rivalry with Groudon.
- Super Mode: Primal Kyogre, which is actually her original form.
- Womanchild: Remarkably immature and lazy for an eons old being.
Groudon
Legendary Pokémon of Hoenn whose existence dates back to the beginning of time. He created the continents, summons harsh sunlight with his presence alone, and has eternal rivalry with Kyogre.
- Manchild: Remarkably immature and lazy for an eons old being.
- Super Mode: Primal Groudon, which is actually his original form.
Rayquaza
Legendary Pokémon of Hoenn whose existence dates back to the beginning of time. He rules the skies, protects the planet from extraterrestrial threats, and quells the eternal rivalry between Kyogre and Groudon whenever it surfaces. Much to his chagrin, the latter takes much more effort than the former.
- Friendly Sniper: His main duty besides taking care of Groudon and Kyogre is to destroy meteorites that could damage the planet, a job that typically involves sniping them before they land.
- Improbable Aiming Skills: Even if it's mostly passed over, he's capable of sniping meteorites from hundreds of thousands of kilometers away to ensure they don't hit the planet. Even if space is a vacuum and doesn't cause his attacks to go off course and he has millions of years of experience, that is very impressive.
- Mundane Utility: His Air Lock ability also serves to make it so that he can "smooth" his attack point so that nothing knocks him off course.
- Purposely Overpowered: After Arceus got pancaked by the dinosaur-killing meteorite, he made sure to over-engineer Mega Rayquaza to make sure that doesn't happen again.
- Super Mode: Whenever he swallows a Meteorite.
- "The Reason You Suck" Speech: Gives one to his two unruly charges after the events of the Delta Episode.
- Time Abyss: He's apparently old enough to remember the meteorite that killed the dinosaurs.
- World's Strongest Man: Besides Arceus (and possibly Ultra Necrozma and Eternamax Eternatus, who have yet to appear), he's Mewtwo's main competitor for the title of "World's Most Powerful Pokemon", and even if Mewtwo is stronger, Rayquaza's sheer experience leaves even the "remembered" Mewtwo's completely in the dust.
Hoopa
A Legendary Pokémon from Kalos. One joins the group taking part in stopping the Delta meteor, helping transport people to the moon.
Lake Guardians (Mesprit, Uxie, Azelf)
A group of Legendary Pokémon from Sinnoh, representing emotion, knowledge and willpower, respectively.
Mesprit first appeared during the Delta Episode, when it was awakened by Dawn and Barry, and it and its two companions got Kyogre to create a rainstorm that deflected the heat pulse from meteor debris hitting the atmosphere. It has taken an interest in Dawn.
They start making more frequent appearances in Sinnoh, where it's revealed that they are responsible for Ash being able to remind people and Pokémon of the previous timeline.
- Ambiguous Gender: Suicine says that they only say that it's obvious whenever someone asks about it, so she just uses they/the, pronouns to describe them.
- Captured Super-Entity: They end up captured by Team Galactic for use in their mission, leaving Ash unable to Remind others (except Giratina, since Azelf managed to sneak his memories to Ash before being captured).
- Spock Speak: Uxie speaks like this, due to representing knowledge.
Deoxys-Blue
A Deoxys who had been in hibernation within the meteor from the Delta Episode, and was completely unaware that it was on a collision course with an inhabited planet until after the meteor was destroyed. As community service, it joined a company to assist with space travel and exploration.
- Mike Nelson, Destroyer of Worlds: Comparisons are made to cruise control running amok after 50,000 years.
- Unwitting Instigator of Doom: How was he to know that if he went to sleep for 50,000 years, the meteor he was using for transport would fly straight into a planet?
Cresselia
A Legendary Pokémon from Sinnoh, who resides on the moon. She was not happy to find a moon base had been set up without her approval, until the people there explained about the asteroid and offered her rent.
- Slept Through the Apocalypse: Slept through the entire Delta episode.
Legendary golems (Regirock, Regice, Registeel, Regigigas (Tree of Beginning)
A Legendary trio and their leader who are in charge of protecting the Tree of Beginning in the Rota Kingdom. The main trio were glitched as a result of years without oversight, but eventually had their systems ''upgraded'' by Regigigas after some prompting from Mew.
- Murderous Malfunctioning Machine: The trio's security recognition software was glitched, resulting in them babbling out computer jargon as they tried to eliminate Ash and Co.
Manaphy
See May's Pokémon
Reshiram
One of the Tao Trio, who was summoned by Team Plasma to join N as part of his role as the Hero of Truth. He gladly joined N as his Pokémon, but drove away Ghetsis and the other Plasma members due to seeing the truth about them being villains and not heroes, something N had come to suspect. The pair, along with some others, are now traveling together to learn more about the world.
- Hopeless with Tech: Poké-balls and suspension bridges are all new things to him. He even kept blowing up the former while N tried to capture him.
- Living Lie Detector: As the embodiment of Truth, he can do this, which is how he could see N's doubts that his peers were being truthful, as well as the deceit in them himself.
Deoxys-Orange
See Max's Pokémon
Meanwhile with Arceus
Arceus
The Creator of the Pokémon universe. Due to Cyrus' plot succeeding, he and Sir Aaron are trapped in a pocket dimension, and it is because of Arceus that Ash received the opportunity to be trained in Aura by Sir Aaron and the one who gave Ash his mission to stop Cyrus via time travel.
- Big Good: Of the entire Pokémon universe. He did create it after all...
- The Chooser of the One: Certainly has the authority to do so. Other Legendaries mention how he chose Ash as his champion when explaining things to others, so there's that.
- King of All Cosmos: He's not exactly all there.
- Medium Awareness: It makes sense for the Creator Of All. He prevents Sir Aaron from talking about what his hat does since the audience doesn't know about it yet. When Sir Aaron questions him on it, he not-so-subtly changes the subject.
- Mission from God: Inverted Trope. He's God and thus is the one who gave Ash the mission.
- Obvious Rule Patch: Often has to do this when Aaron and the Creation Trio find a loophole.
- Reality Warper: Creates pocket realities for Aaron and Creation Dragons to pass the time until Ash saves the world.
- Sealed Good in a Can: He and the others are in a pocket dimension that's within the G.S. Ball. Ash finally figures it out and sends them out to deal with the original timeline's Cyrus and his team.
- Throw It In!: How the Fairy-type came into existence, thanks to a Sylveon (Molly's Eevee) being present at the creation of the world. It utterly baffles Norman when he hears about it.
Sir Aaron
Master of Aura and is currently Arceus' roommate in the pocket dimension they are trapped in.
- Back from the Dead: Sort of. He's in a pocket dimension but he is by definition dead. Then properly revived when he's released from the G.S. Ball with the rest of the group, albeit still as a Riolu.
- Forced Transformation: In typical fashion, when Arceus creates the Mystery Dungeon verse he becomes a Riolu. He's still one when he and the others are released from the G.S. Ball.
- Only Sane Man: Of the pocket dimension inhabitants.
- Shout-Out: While pretty much any usage of Bone Rush ends up being a Fate Series reference, Sir Aaron apparently became famous because of his sheer mastery over the move, being able to create weapons - specifically, a pair of falchions made from the concept of brotherhood. Yes, Sir Aaron's Signature Move is to create Kanshou and Bakuya and then perform Archer's Crane Wing Three Realm.
- Token Human: Trapped inside the pocket dimension with Arceus and the second Creation Trio as the only human. At least until he becomes a Riolu which seems to be permanent now that he's been released from the G.S. Ball, essentially reincarnating him into the world.
Palkia, Dialga, and Giratina
A second copy of the Creation Trio that Arceus created to send Ash back in time.
- Forgot About His Powers: Dialga and Palkia once forgot that they could fly up a set of stairs. Giratina remembered immediately.
- Manchild: Justified, since they've only very recently been created. It's to the point that they address Arceus as "Dad" (which makes Arceus nostalgic, as their counterparts haven't called Arceus that in literally forever). Arceus even distracts them while they're waiting in the pocket dimension by having them play various games (aka games that aren't from the main line of Pokémon video games, such as Mystery Dungeon).
- Oh, Crap!: Their reaction when they learn about the Fairy-Type being completely immune to the Dragon-Type. That immunity ends up confusing Original Cyrus when Ash's Mawile completely ignores Primal Palkia's Spacial Rend.
- Dialga is very relieved to learn that the Fairy-Type is vulnerable to the Steel-type.
