"I think back on those peaceful days we took for granted. When our genocide wasn't even conceivable, when killing a Pokémon was crazy, when a simple Ember didn't end in 3rd degree burns, and when I didn't worry about whether I would live to see morning."
A Million Is a Statistic: Uxie adopted this mindset to cope with the countless wars he's seen over the years. This is also shown to be why he isn't fazed in the slightest at the idea of killing all of the Grimer and Muk.
It later expands to all poison-types using Gengiga.
As well as Magcargo and Slugma using the Metagross and Alakazam.
He's planning on cloning them all once he's modified the extinct species to no longer have their harmful effects.
Keep in mind that any of the characters in this fic can die. Even if they're main characters. I think I already proved that with Sabrina.
Don't forget the trainers' Pokemon. After The Subsistence, it has practically become a rule that a main character has to lose at least three Pokemon.
Arc Villain: Gengiga acts as the main threat against the heroic Legendaries during The Defervescence.
Armor Is Useless: Averted. Samurai is the only armored character in the fic and his armor has saved him from the Beedrill attacks.
Asshole Victims: The Muk that attacked Hearthome were much more cunning and deliberate in their wiping out the population of the city. With that in mind, it's hard to feel sorry for them after Gengar absorbs them all.
Harley's Banette went down this path as well, but seeing the Houndoom afraid of him after he torments, roasts and explodes a Golem purely for his own amusementsnapped him out of it. He's very afraid he will act just like he did next time, but an Earthquake from a particularly powerful Golem injures him fatally before he can do it again.
Rico could have went this way but he decided to make an Heroic Sacrifice to let the rescue party escape before he could snap.
My pack is strong. You may have taken many of us, but not all of us are gone, and you will not take another! I will show you their strength, for I carry it on my back! I will defeat you for those that have fallen!
Uxie gives one in his own way after his Batman Gambit comes to fruition:
There was now little to nothing that could stop him, and that which could would be dealt with swiftly and mercilessly before it even realized it could even prove to be a nuisance to him. The universe demanded diversity, and Uxie would make sure to catalogue it before he was forced to subtract from his equation.
Batman Gambit: Uxie sending Ho-Oh into the Reverse World was a gambit to get Giratina to capture him, even using the reflective surfaces since it was his method of viewing their world. Once he did, Uxie sent Rayquza in to fatally injure him and attain a sample to clone him, all so that one of the few beings that could seal him away was contained. The only thing he didn't predict was Ho-Oh choosing to stay in the Reverse World rather than returning and being his experiment.
Arceus warns Lugia of this when he entrusts him with the orbs of creation. He doesn't listen and creates a brother when he started to feel lonely. At the start it's happy but he still feels that something is amiss, then he learns that what he really wants is a mate. After dreaming with a perfect mate, he makes a wish with one of his orbs and he gets her. His brother leaves them after Lugia decided to use his last orb to give his mate the ability to procreate instead of giving him a mate too, damning him a life of solitude. He would join Ho-Oh's cause in the future.
The Rant of Chapter 8 of The Defervescence has Cornova call out the readers on this:
Over the years I've had so many people repeatedly tell me how much they wanted me to get rid of Ho-oh. So now, there you go. For those of you who wanted it, I hope this sates you. Because now, now you'll simply have to deal with the one who's taken his place, and he's not going anywhere.
Beware the Silly Ones: Mew is very childish but he can transform into any Pokémon he desires and every attack is his to command. To top it off, he can teleport at will.
Big Damn Villains: Near the end of Start of Chaos, Alakazam's attack on the hideout Dawson's group is taking refuge in is halted when Team Rocket swoops in on them. It sort of helps that the hideout belonged to the group, and justified because they detected a signal there. To be specific, it's the one near the Lake of Rage.
Black Comedy: Banette's favorite coping mechanism. This exchange from when he died and came back to life pretty much says it all:
Banette: All I remember was everything being white for as far as I could see. I don't know if I imagined it all, if it was a dream, or if I really died. What really surprised me was that there weren't any flames.
Banette: Oh come on, you didn't honestly think I was gonna end up anywhere else if I died, did you?
Blessed with Suck: Dampener removal greatly augments a Pokémon's abilities. Unfortunately, it is extremely painful and results in Power Incontinence until they learn to control it. Even then, their attacks are always lethal and extremely destructive. It is especially magnified for Pokémon like Heatran or Magmar whose body temperature rises to such an extent that being near them is lethal.
Blood Knight: Pikachu becomes one for a short time in The Coalescence.
AJ in The Subsistence made it clear that he'd kill any Pokémon that attacks humans.
Bloodstained Glass Windows: The survivors in Hell In Sinnoh take refuge in a cathedral and one of them curses Arceus for allowing this war to happen. The last "shot" is that of the broken stained glass windows.
Blue and Orange Morality: Uxie's code of morals isn't based on any idea of good or evil, but rather what is and isn't logically the best outcome. This leads to him making very ruthless decisions for Ho-oh's side, but he doesn't even see them as ruthless; to him, they're the most logical course of action and therefore the best.
Boom, Headshot: This is how Suicune dispatches a number of people inside a Pokemon Center.
And how Alex dispatches the gang leader on Rustoboro City to save Katrina from a certain death.
Also happens to Weavile in The Truculence after he sees the giant Gengar (Gengiga) wipe out an entire group of Muk.
Bunny-Ears Lawyer: Dr. Kaminko from The Pokémon They Carried has a habit of naming his military hardware after Pokémon. Command lets him keep doing this because he's just that damn good at designing weapons.
Can't Hold Her Liquor: In a party at the end of The Coalescence, Dawn gets completely shitfaced on a very weak alcoholic drink. Justified by her young age.
The Captain: Alpha clearly serves this role for the Houndoom pack.
Cerebus Retcon: When Gengiga and Alakalossal appeared in the anime they were just whacky Filler Villains that parodied giant monster movies. Poke Wars explores just how dangerous two giant Kaiju could be in a more serious work with no Dues Ex Machina Jigglypuff to stop them. For example Gengiga effortlessly committing a genocide of Poison Pokemon in Sinnoh and all four Regis were needed to stand up to his Superpower Lottery.
Chainsaw Good: Duplica's Mini-Dit can transform into a chainsaw katana.
Character Development: Harley is a good example. At first he's a Jerkass who tells the police that May killed all the people in the contest hall on purpose for no reason other than to cause her problems. Until his own Pokémon start dying, that is. He mellows out even more afterwards, and even prays for May and Drew to die quickly and/or without pain when their situation looks particularly hopeless.
A Chat with Satan: Happens in The Defervescence where Giratina meets Ho-oh in the Reverse World and calls him out on all of his atrocities.
Celeb Crush: Angela feels this kind of crush on Arthur, after seeing him participating and winning the second place of the Ever Grande Conference.
Chestburster: Weedle reproduce by stinging their host and impregnating them with their offspring, which then proceed to eat their host alive. Wurmple use a variation of this with the same disturbing effects or even more.
Child Soldiers: If Dawn of a New Era is any indication, a decent portion of the soldiers are teenagers or possibly even younger.
And let's not forget the title character. She's fourteen at the time of the story.
Cluster F-Bomb: The Golem in chapter eight and nine of The Exigence swear far more than any other characters.
Combat Breakdown: Present in practically every fight so far. The only exception was Pikachu vs. Sandslash, since (despite everything) it was just a spar.
Convection Schmonvection: Averted by Paul's Magmar in The Truculence. When he first emerges from the Pokéball, he gives off so much radiant heat that Paul's Honchkrow bursts into flame. In fact, he produces so much heat that he melts a stop sign just by walking past it.
Crapsack World: Pretty much everywhere, but Johto got the short end of the stick so far, as it was the epicenter of the war and the place Ho-Oh's crew bore down on humans the hardest. It becomes the Big Bad's base of operations later on.
Death World: No place is truly safe anymore for either Pokémon or humans.
Deconstruction Fic: This series completely tears apart the sub-genre of Pokémon revolution fanfictions. It also highlights how lethal the Pokémon can be.
Deus Ax Machina: In Dawn of a New Era, Ash finds a fire ax inside the Celedon City gym and uses to break down a locked door.
Do Not Do This Cool Thing: The effects of the war are depicted realistically and there is a fairly obvious War Is Hell message. Unfortunately, few of the reviewers notice this, instead choosing to focus on the elaborate fight scenes.
Doesn't Like Guns: Ash and Samurai refuse to use firearms, but it doesn't stop the former from using them.
Doorstopper: The shortest one of the completed books is 55,073 words long. If all the completed books are added up together, they total 340,186 words.
Downer Ending: The Defervescence ends on this note - Ho-oh realizes his mistakes too late and is forever trapped in the Distortion World, Uxie has complete control over Ho-oh's army and is no danger of losing it, Mesprit was on the verge of a mental breakdown after recruiting the Gardevoir and the Gallade, and Arceus appears before Azelf just long enough to explain why he won't ever return to their world even after the war ends.
Drop Ship: The Pelipper class dropships featured in The Pokémon They Carried. It should be noted that these drop ships are designed for atmospheric use.
Drop the Hammer: Andre from Downfall of a Champion fights with a sledgehammer.
Emotions vs. Stoicism: On Lugia's side, we have Mesprit, the living incarnation of emotions that is clearly shown suffering after seeing the atrocities of the war-torn world. On Ho-oh's side, we have Uxie, who sees emotions as a distraction in the way of his experiments.
Even Evil Has Loved Ones: Entei is a sadist that takes great pleasure out of making games out of his slaughter of humans and trained Pokemon alike, but he loves his brothers, and would gladly give his life for them.
Even Evil Has Standards: Subverted. Ho-oh is at first horrified at the concept of wiping out the entire species of Grimer and Muk. He only goes along with it after hearing Uxie's reasoning, justifying it to himself with the rationale of those Pokémon being by-products of humanity and therefore an extension of humans.
Ho-oh also despises clones, which puts him at odds with Uxie when the latter decides to start utilizing New Island's cloning technology.
Poké Wars: La Supervivencia (Poké Wars: The Survival) which tells the story of a group of survivors from Petalburg City who are trying to find a safe haven from wild Pokémon, introducing both known (Brendan and Max for example) and new characters to the story.
Expendable Clone: Uxie aims to use the cloning technology to create an army of clone Pokémon - that way, whenever Ho-oh's coalition goes to war, whatever losses they incur will mostly be clones as opposed to actual Pokémon.
I305 "Lairon" Mobile Infantry Self-Contained Pressurized Environmental Combat Survival Exoskeleton from Poké Wars: The Divergence seem suspiciously similar to the MJOLNIR suits that Master Chief wears.
Fallen Hero: The Defervescence shows that while he was always a bit egotistical, Big Bad Ho-oh used to have his heart in the right place.
Fastball Special: A variant. Regigigas throws Regirock at Mewtwo not as a blunt projectile but as a grenade.
The Dragon: Raikou: Ho-oh's "lieutenant", who accompanies him at nearly all times.
Entei: Another one of Ho-Oh's dragons, sent on a mission to recruit wild Pokémon.
Kyogre: Has so far been commanding the majority of the underwater Pokémon to do Ho-oh's bidding, and has also discovered an "ace" that supposedly could guarantee Ho-oh's victory.
Dragon-in-Chief: Uxie is a far more competent antagonist than Ho-oh lacking Ho-oh's Smug Snake ego. He's the one who constantly upgrades and expands Ho-oh's forces, keeps all of the megalomaniacs that Ho-oh's recruited in line, and basically makes all the plans. Ho-oh has recently realized this and is fearing that he might soon be Demoted to Dragon. Although Uxie just tosses him into the Reverse World and effectively takes over.
The Brute: Shadow Lugia: A corrupted Lugia clone who only desires to take the real Lugia's mate and cause as much destruction as possible.
Evil Genius: Uxie: The Being of Knowledge who sees the genocide and everything else as a chance to experiment. He's doing it For Science!, though, and only joined Ho-Oh because he won't complain about Uxie's lack of morality.
Dark Chick: Mewtwo: An artificial being who first fought against Ho-oh and lost, ending up as little more than a mind controlled puppet.
Fork Lift Fu: Andre from Downfall of a Champion uses a front end loader to break out of an abandoned warehouse.
For Science!: Uxie's sole reason for joining up with Ho-oh; he wants to use the war and genocide as a chance to experiment.
Freudian Excuse: Shadow Lugia is pretty ticked off about the abuse he suffered under Cipher.
The other hostile Legendaries, save Kyogre, have pretty "legitimate" (in their eyes) reasons to hate humanity.
From Bad to Worse: Ho-Oh is usurped by Uxie, who sees everything as an experiment and is far crueler and smarter than any other character due to his lack of emotions.
The Gunslinger: Dawn. She's a combination of Type A and a little of Type C.
Hellfire: Will-O-Wisp is a supernatural purple-blue fire that cannot be extinguished and can burn even rock.
Heroic BSOD: May, believing her Pokémon have killed an entire contest hall full of people.
Whitney after she finds her uncle's corpse.
Tracy, after losing all the Pokémon on the ranch because of the Muk, along with all the spare pokeglovs and everything else important to him. He even wished Ash would die.
Heroic Sacrifice: Sabrina sacrifices herself to teleport everyone to safety after Pikachu ignites the volatile gas filled air surrounding a city overrun by Grimer and Muk, which becomes a massive fireball.
Solidad drops off Drew's Flygon, allowing Drew and Harley to escape Raikou's attacks, which the Pokémon couldn't evade due to the weight.
Harley's Ariados tackles Harley out of the way of an Ursaring's Hyper Beam. He gets the bottom half of his body vaporized in the process, but gets rid of his blinding bloodlust.
Rico buys time for a rescue party to carry back captured people from a Beautifly and Dustox attack, he accomplishes his objective but is killed by a Beautifly's Silver Wind attack.
Gengiga. He singlehandedly killed a regions worth of poison Pokémon, was more powerful than most Legendary Pokémon, heck, other Legendaries feared him. And it took all four Regis, being drowned in lava on top of him wanting to die in order too kill him.
Hope Spot: Rayquaza encourages Lugia's brother not to destroy Olivine City under this rationale - if it's left intact, then more and more humans will see it as a place of refuge and flock to it. Then, whenever Ho-oh or one of his allies returns, there will be far more humans to kill.
Hostage Situation: The caravan has to confront a gang from Rustboro City who have taken some people as hostages, wanting to exchange them for all their supplies and weaponry.
Darkrai: Humans are conquerors; whether it with is Pokémon or with each other.
Hypercompetent Sidekick: Uxie to Ho-oh; Ho-oh even admits that the sprite is the only real reason that his plans haven't completely fallen apart. He eventually takes over.
The Hyena: Banette has a habit of bursting into laughter at random and usually inappropriate moments. Or when he's called out on it.
I Am Not Left-Handed: Halfway through his fight with the Regis, Gengiga reveals that he hasn't been using the moves that Uxie taught him.
I Call It Vera: Kaiza's custom built revolver is called "Thunderbolt".
I Did What I Had to Do: In The Subsistence, Ash has Pikachu use Thunder on a sinking ferry overrun by Sharpedo and Tentecruel. He regrets that he had to kill everyone on the ship but the Pokémon swarming the ship were too dangerous to leave alive.
Hiiro in Fool's Paradise has his Ampharos unleash Thunder in a harbor filled with Tentacruel and their victims, killing everyone in the water so the boats in Olivine City can head out to sea. He calls his plan "a horrible, despicable, but ultimately necessary idea" and he explicitly states "You won't like it" to an Officer Jenny who asks him for a plan.
Alex said this to Katrina back on the caravan's encampment after rescuing her from a Hostage Situation.
I Die Free: Gengiga prefers death than to remain under Uxie's thumb.
Invulnerable Knuckles - averted with a vengeance in chapters 8 and 9 of The Exigence. It looks like Blaziken will take a long while to recover after breaking both hands and one leg while attacking the Golem.
Just Between You and Me: Ho-oh reveals to Mewtwo during their battle that the dampener removal gave him the subtype of Dark and therefore made him immune to Mewtwo's psychic attacks. Mewtwo promptly uses Miracle Eye to negate that advantage and then uses Psychic to tear Ho-oh's head and limbs apart.
Kamehame Hadoken: Batuo and his Medicham are confirmed to be able to do this, being called a Chi Wave.
Killer Rabbit: Uxie should be on the top of everyone's "Do Not Fuck With" List if you value your life. Even Ho-oh fears him.
Kill It with Fire: What fire-type attacks now do. Will-O-Wisp is a particularly horrifying example, as it cannot be put out except by the attacker's will.
Kill It with Water: Water Gun and Hydro Pump are now capable of dismembering their targets.
Knight of Cerebus: While this fic was never Pichus and Clefairys, the arrival of the Muk truly set the toneof this story, causing the first main character deaths outside of secondhand accounts and flashbacks.
Uxie ups the ante a billion fold, with his skills turning Ho-oh's failing plan and organization into a cold, cruel, Lawful Evil army of Hero Killers.
Kung-Fu Sonic Boom - When Regigigas punches Ho-oh, the shockwave produced blows a crater in the ground.
The punches of Slakings produces small craters to show how strong they are.
Jerkass Has a Point: Paul has Marcie's corpse thrown off the train they're on to distract the Drapion despite everyone's protest because they needed the time, there was no way to know if she was contaminated, and they can't afford dead weight.
La Résistance: Lugia's corps of Legendaries and Ash's band are the biggest examples.
Last Stand: Implied by Harley's Banette that it'll be their way to go when May's group gets surrounded by a pack of Houndoom. Thankfully, they come in peace.
Leave No Survivors: Ho-oh orders Raikou to do this when Raikou launches his attack on Goldenrod City; Raikou takes it so much to heart that he relentlessly blasts the nearby ranch where May, Whitney, and Drew are taking cover after he's killed everything else in the city.
Lethal Harmless Powers: Thanks to the dampener removal, many "harmless" attacks and abilities can be used in lethal and gruesome ways. Some examples:
Banette can phase through solid matter (including living things) with ease. Combine that with Will-O-Wisp and he can start fires inside his victims.
Gravity originally immobilized its victims and forced flyers to land. Now it can also be used to crush a target to death or turn rain into dangerous projectiles.
String Shot originally bound and immobilized its victims. It can now be used as Razor Wire.
The Carnevale Masquerade comination move as used by Roserade and Masquerain consisted of a beautiful dance combined with a shower of petals and a sweet odor. It was intended to be used as a flashy non-damaging move in a Pokémon contest. Using against a horde of bug Pokémon resulted in Pink Mist.
Life or Limb Decision: A Golem in The Exigence smashes his frozen arm to keep the rest of his body from freezing over.
Literal Genie: Wishes made on an Orb of Creation must be worded very specifically; Lugia finds this out the hard way when he realizes that although he wished for a mate, his wish did not mention anything about the mate being able to procreate. He ended up using his final Orb to give her that ability, which in turn leads to his brother's Face-Heel Turn.
Ludicrous Gibs: Not surprisingly, most Pokémon attacks now result in this. Shotgun shells on smaller Pokémon have about the same effect.
Mad Scientist: Uxie sees the entire genocide/war as nothing more than a science experiment. And there are implications that he wants to clone Ash.
Man Child: Mew is not exactly a bastion of maturity. As evidenced by his words upon meeting Latias.
Mew: Hi. I'm Mew. Wanna play?
Mass "Oh, Crap!": Ash and co. in The Subsistence when they realize that not only does Bill's Dragonite Call still work, the giant Dragonite that was called is pissed off.
Mass Super-Empowering Event: Aside from the one affecting the Pokémon, Lugia uses his own orb of creation to remove the dampeners of humans.
Mercy Kill: Ash to the unfortunate survivors in the sea of murderous Pokémon and Kaiza, and Samurai to his Pinsir.
Mighty Glacier: M1-12 Rhydon cargo carriers mount one 105 mm smoothbore cannon, several 30 mm autocannons and are heavily armored enough to shrug off anything short of a Hyper Beam or Legendary Pokémon attack. Their top speed is twenty five miles per hour.
Military Fiction: The Pokémon They Carried, Dawn of a New Era, The Divergence, and Amidst Chaos have elements of this genre.
Military Mashup Machine: The M1-12 Rhydon cargo carriers mentioned in The Pokemon They Carried are "small" land battleships. They weigh 136 tons, stand 14 meters (46 feet) tall and are armed with 105mm smoothbore cannon on a mount that can rotate 360 degrees along with a bunch of turrets bearing 30 mm autocannons. Oh yeah, they can also carry supplies and troops. And they have armor that is impervious to anything short of a Hyper Beam or Legendary Pokémon attack.
Mind Over Manners: Sabrina forgets this being so happy to meet Ash again, Lt. Surge and Samurai attempted to kill her. Not to mention the way she embarrassed Misty and Dawn...
Mind Rape: Uxie harvests knowledge human scientists minds before killing them.
Mon Puppets: Ho-oh takes control of Mewtwo's body with an orb of creation.
Never Got to Say Goodbye: Roserade was greatly annoyed by Banette, and let out some pretty harsh words to him before he went out to help the Houndoom. She gets very upset when she finds him (briefly) bereft of life in the battlefield, and recognizes that, despite her dislike of his antics, he was the only one that managed to pull their group out of the depressed moments they'd faced so far.
Nice Job Breaking It, Hero: Regigigas and his trio successfully kill Gengiga, assuming Ho-oh had deployed him to attack Lugia and co. If they hadn't done so, Gengiga would have eliminated the poison-types in Kanto, including a certain cluster of Muk…
Nothing Is the Same Anymore: Forget most of what you would find in the Pokémon series - there is no Pokémon capturing, badge collecting, contests, rivals, nothing. After the removal of the dampeners, the characters' lives become more similar to Prisoner 849's time in Na Pali than anything else. The Pokémon They Carried has a general atmosphere closely resembling the Command & Conquer series.
Not Quite Dead - Heroic example. Banette gets smashed into a tree by a rampaging Golem and "dies" in Clefable's hands. He comes back to life when the group's Pokemon cry over him, bringing him back with Pokémon tears.
Obliviously Evil - Muk only wish to expand their territory, and any sort of ecological damage they may cause is completely unintentional on their part.
Out, Damned Spot!: Suicune goes right into this trope after personally killing quite a few humans.
Pin-Pulling Teeth - Ash pulls the pins of some grenades he stole from Kaiza and then blows up a bridge to keep the Cloyster from attacking him and Dawn in The Coalescence.
Plot Armor - Judging by the Expanded Universe stories, which show the future of the series' world, most of the Kanto arc characters, including at least Ash, Surge, Dawn, Samurai, and Duplica survive and stay sane enough to occupy important posts at the new human coalition.
Powered Armor - the I305 "Lairon" Mobile Infantry Self-Contained Pressurized Environmental Combat Survival Exoskeleton mentioned in The Divergence provide protection against extreme environments and battle damage in addition to substantially increasing the wearer's strength.
Power Incontinence - A lot of trainer Pokémon accidentally kill their allies when the dampeners are removed, including Lt.Surge's Raichu and AJ's Sandslash. The Psychics in Saffron killed everyone, including themselves with the exception of Sabrina.
Razor Wind - Aside from the standard Razor Wind and Air Cutter attacks from the Pokémon canon, Samurai eventually gains the ability to swing his katana with such force that he can generate a blade of air.
Beautiflys can use Silver Wind with deadly effect.
Reality Subtext: One chapter of ''The Defervescence has Uxie succeed in getting Mewtwo to transform into his mega form. The day before that chapter was uploaded was the day where the advanced forms were officially revealed to be called "mega forms."
In Dawn of a New Era Dawn, get the nickname "Blue Death" for her skill with a .50 caliber sniper rifle. She doesn't like it.
Hiiro Mizutani from The Pokémon They Carried bears the nickname of "Black Blade".
Mimoru from The Pokémon They Carried is known by the soldiers as "The Marionette".
Gengiga is known as "The Life Engine".
Uxie is "The All-Knowing".
Removed Achilles Heel: Uxie murders the giant Jigglypuff that can seal Gengiga and Alakalossal leaving them completely unchained and nigh-unstoppable.
The Resenter: Shadow Lugia is very much this towards the original, and Ho-oh goads Kyogre into being this towards Manaphy.
Resurrective Immortality: Ho-oh has been thrown into a mountain and had his limbs and head torn apart, and come back none the worse for wear. According to Uxie, only a legendary is able to have this ability - if a normal Pokémon had it, they'd fall under Born-Again Immortality. When Uxie decides to take over he mentions several ways to negate it before tossing him into the Reverse World.
The Rival - Sandslash and Pikachu had this going on in The Coalescence.
Rule of Cool - The battle sequences practically run on high-test Rule Of Cool.
Sanity Slippage: As Suicune kills more and more people, his sanity has notably deteriorated. It has gotten to the point where he is hearing voices and it's only the second chapter of his story!
Rico did know he was slowly slipping after his traumatic experience on the pokemon center basemant. So he decided to pull an Heroic Sacrifice to avoid becoming a danger to the caravan.
Ho-oh is a great and noble angelic being of light who's Pride makes him rebel against God's chosen plan in favor of his own vision and he makes other Legendaries/Angels join him by preying on their hidden desires and his fall to evil causes him to lose sight of what he originally fought for turning him into an angry, spiteful, and petty creature of darkness, that gets trapped inside the Pokemon version of Hell, the Reverse World.
Uxie is a monster that is sealed away and is released during an apocalyptic scenario who then proceeds to manipulate events from behind the scenes to his benefit, he is a creature that looks like a creature of good and light disguising his evil intent, he believes that he can make the universe superior to God's attempt, and he plans on making mockeries/clones of His creations to act as his army.
The Scapegoat: both May and Harley become this. To put it more clearly, after May's Blaziken destroys the Pokémon contest in a fit caused by his undampening, Harley goes to the police and accuses May of doing so intentionally. The government forces, trying to quench the populace's hunger for any sort of action, gladly goes after her. Why Harley became wanted is unknown, however.
Scenery Gorn: Any description of the attacks will go into detail about how much the surrounding environment has been ravaged. The aftermath of Pikachu and Sandslash's "sparring match" in The Coalescence is a particularly detailed example.
Screw the Rules, I'm Doing What's Right - The Houndoom pack agreed with Entei to attack humans in Ho-Oh's favor. They're not inclined at all on doing so, though - they just agreed to get rid of his overwhelming presence.
Seppuku: In Chapter 19 of The SubsistenceSamurai stabs himself with his own katana, killing the Golbat that leaves him near death.
Serial Escalation: Each battle is more destructive than than the last, and frequently has more casualties.
Shapeshifter: Duplica's Ditto can transform into Pokémon, clothes and even humans and will look and act exactly like the real article. Mini-Dit can transform into any weapon it touches, including firearms.
It's implied that Kaiza went crazy when he had to kill the Safari Zone's Pokémon to ensure his own safety.
If Dawn Of A New Era counts as canon, the eponymous girl also counts. She has an obvious case of PTSD, constantly remembers her times as a Coordinator before the events of the series, and is very bitter about only being recognized by the abilities that gave her the nickname "Blue Death".
Ship Tease: In the The Exigence, Drew and May end up sharing a room and May hints that something may be up between the two.
In The Coalescence there is a scene where Misty kisses Ash. It's actually Duplica's Ditto, but since it copies the person's personality, it counts.
"Is the length okay?" Ash studied himself in the mirror once more. "The length's fine." "How about the style?" "The style's fine, just make it a little cooler." Misty rolled her eyes and sighed, repositioning her hands to her hips. "Just telling me 'cooler' isn't helpful. Give me something to work with. How much is a little?" "It needs to be like fifteen or twenty percent cooler?" Ash offered sheepishly. "You're impossible sometimes," the red head grunted.
His actions in The Deferevescence are practically a deconstruction: he sees everything as a huge equation, and is perfectly willing to "subtract" something from the equation if he decides that it's going to be an impediment (not to mention that he refers to the others in Ho-oh's team as "lab members.") His Lack of Empathy, meanwhile, makes him unable to comprehend why others could have a problem with his actions, such as Ho-oh being upset by something such as wiping out the Grimer and Muk, or trying to clone Legendaries, or Lugia's brother lashing out violently to Uxie reading his mind.
Taking You with Me: One of the Golems in The Exigence tries to pull this with Explosion. He fails, thanks to Clefable's Light Screen.
Terse Talker. Uxie prefers to speak in short clipped sentences, since he thinks talking wastes time when you could advance progress instead.
There Is No Kill Like Overkill: Not content with simply killing all of the humans in and near Goldenrod City, Raikou decides to completely level it, to the point where there's not as much as a pebble for miles around him.
Token Evil Teammate - Groudon only joined Lugia's coalition because Kyogre's joined Ho-oh. Not to mention, he's one of the ruder members.
Too Powerful to Live: Sabrina was too powerful to be introduced so soon. There was no way she was going to survive.
Gengiga for the villains, he could absorb any opponent by looking at them, was powerful enough to carry out a genocide by himself, and had countless extra lives from each life he absorbed just in case those powers weren't enough. He wasn't going to be around long.
Underestimating Badassery: Sort of; Uxie speculates in The Defervescence that Ho-oh has been utilizing only ten percent of Mewtwo's full potential, and the only reason Mewtwo didn't go all out during his battle against Ho-oh was that he himself didn't realize how much power he was actually capable of utilizing.
Undying Loyalty: The Legendary Dogs (especially Raikou) pledged this to Ho-oh, while the giant Alakazam swears this to Uxie.
Unsuspectingly Soused - During the party at the end of The Coalescence, Dawn drinks "soda" that gets her completely drunk. It should be noted that the "soda" was actually a very weak wine cooler or mixed drink.
Villain's Dying Grace: Ho-oh had the option of escaping the Reverse World at the cost of being Uxie's lab rat, he chooses to stay — not because he fears Uxie — but because he genuinely wants to atone for his sins.
Villainous Rescue: At the finale of Start of Chaos, Dawson's party, which also consists of Lance and Clair, are rescued from Alakazam's army by Team Rocket.
Voice of the Legion: Giratina's voice is described as "dozens of voices speaking in some unholy chorus and echoing from the darkest corners of the world".
Warrior Monk: Arthur and his master are the Asian type mixed the Aura Guardians from the pokémon lore.
The Watson: Alakalossal briefly serves as one so Uxie can explain his plan to kill Giratina.
Well-Intentioned Extremist: Ho-oh. He wants Pokémon-kind to live in a utopia… and he does so by engaging in a genocide against humanity.
At least until he went Jumping Off the Slippery Slope by doing things like ordering wanton killing of Pokémon contrary to his ideals, utterly ruining the environment and not giving a damn about it, and generally being a filthy hypocrite.
And then it turns out that his wish applied not just Earth, but the entire galaxy and beyond, as revealed by Giratina.
War Is Hell: The effects of the supercharged Pokemon attacks are described in graphic detail, as well as the feelings of the victim if it's still alive after the hit. The characters' reactions to the more trauma-inducing happenings are just as vividly written.
Weaksauce Weakness: Subverted with Uxie, who claims that reflective surfaces are his since he'd see his own eyes and have his own memory wiped. However, it's hinted later on that his eyes have atrophied to the point where he can't see anything, including himself, if he did open them.
We Have Reserves: A majority of wild Pokemon are extremely guilty of this trope. The alphas tend to throw waves of mooks at the heroes like they're extremely cheap confetti. Tends to overlap with Attack! Attack! Attack!.
Uxie has now pulled this trope on Ho-oh, having deemed him too incompetent to properly lead the genocide and has sent him on an all expenses paid trip to the Reverse World with no return ticket. Yes, The Dragon has pulled this trope on the Big Bad. Be afraid. Be VERY afraid.