* CompleteMonster: Deoxys, the BigBad. [[EstablishingCharacterMoment His first action]] after coming to earth is murdering and torturing a small Pokémon child after his twin was just murdered before his eyes. Over the course of the story, he maims, murders, slaughters, mutilates, and does everything in his power to make the heroes' lives a living and total hell. He nukes several heavily populated areas around the world with his virus to acquire more mindless minions for his goal (and every single one of his minions is in agonizing pain every second they're existing) and will do everything and anything to punish those who gets in his ways. In fact, he sums it perfectly when questioned why he does all of his atrocious acts.
-->'''Deoxys''': Because it is my wish. Because they were in my way. And most importantly, because I can.
* CrowningMomentOfFunny: The cast enjoys a quiet-before-the-storm party on the night before the final battle. Some of them go for more...[[PreClimaxClimax involved]] celebrations than others. So anyway, [[ChildrenAreInnocent Phanpy]] walks in on [[ItMakesSenseInContext Uncle Brother]] Pikachu going at it with a Weavile. Traumatized, he runs to Aunt Corsola for help, and walks in on ''her'' right in the middle of [[LovableSexManiac Crawdaunt's]] ''massive orgy''. You can [[HarmfulToMinors probably]] [[BlankWhiteEyes imagine]] [[HeroicBSOD what]] [[TraumaInducedAmnesia happens next]].
* LesYay: Misdreavus and Umbreon.
* LoveItOrHateIt: You either love it because of the epic fight sequences, and acts of unbelievable badassitude...or you think it's the ''Agony in Pink'' of the Pokemon fandom.
* MoralEventHorizon:
** Deoxys crosses this when he destroys an entire city, personally striking down the Pichu Brothers.
** [[spoiler: Ford has his partner Blaziken brutally torture Charizard, and turns Ash into Alpha Ranger.]]
** Mariah nearly destroys May's psyche during their battle with her insults.
** Dark Latios [[spoiler: torments his sister, kills their father Ho-oh, kills Lady Ho-oh by ripping out her spine and eating her body, force-feeds Latias her father's genitals(!), and then repeatedly rapes her both physically and mentally until she becomes an emotionless killing machine.]]
* OT3: A particularly weird HotSkittyOnWailordAction example: [[spoiler:Wobbuffet, Milotic, and Cacturne]]. You may now scrub your brain with peroxide.
** If one recalls properly, it becomes fairly obvious that [[spoiler:Groudon / Kyogre]] is really a case of [[spoiler:Groudon / Kyogre / Groudon's awesome pants.]]
* ShippingBedDeath: Refreshingly averted. Ash and Misty hook up quite early on, and their [[HappilyMarried ongoing relationship]] is handled as a an integral part of everything happening around them.
* {{Squick}}: The descriptions of the undead/mutilated Legendary Beasts. ''Ugh''.
** It gets to the point during the final arc where one of the ghastly settings is actually discarded as "kind of so-so as far as generic hellscapes go".
** The final arc has [[FamilyUnfriendlyViolence no]] [[{{Gorn}} short]] [[CruelAndUnusualDeath supply]] of this.
* ShockingSwerve: In the final chapter it's revealed that [[spoiler:Mewgle had trapped everyone - and we do mean EVERYONE - in virtual reality so he could take over the multiverse. It winds up {{Retcon}}ning generally a lot of things.]] Some readers found that it [[AuthorsSavingThrow gave more closure to the story]], while others thought that [[AssPull it made everything worse]], and that the author should have left it alone.
* ShowDontTell: The natural consequences of the {{Infodump}}s. There's a lot of background information that would have been better in a flashback. Some examples include Lady Ho-Oh's StartOfDarkness and Mewtwo's first encounter with Deoxys - thanks to the {{Infodump}}s, they're reduced to OffstageVillainy.
* StrangledByTheRedString: Latias and [[spoiler: the Ghost King's]] relationship is the most complained about aspect of the story. From the very beginning of the story, Latias [[spoiler:has been dreaming about marrying the Ghost King, even though she didn't know what he even looked like. Later on, she forgives the him for razing her hometown and murdering everyone in it in a childish fit of rage, because two out of the hundreds of thousands of innocent dead said they forgive him. And then Latias marries the damn guy!]] Many readers were not at all satisfied with the story's explanation [[spoiler:and especially not the tacked-on revelation that Kyogre secretly made the Ghost King do it at the very end]], and consider this a Wall Banger.
* WhatAnIdiot:
** So you want to try to apologize to your crush for destroying her city, killing all her friends, and ultimately traumatizing her. You can't go anywhere, so you need someone to convince her to come to you. So you send out your most loyal servant...who is also the one who killed your crush's best friend right before her own eyes. Oh, and he's also a {{Jerkass}}, and would rather terrorize her for several days instead of just bringing her right to you.
** Fearow's gimmick is that he eats other Pokemon and gets stronger from it. So what happens when his minions capture Latias? Does he immediately grab some bread and have a dragon-on-rye sandwich? Nope, he tries to [[GratuitousRape rape her for no reason]], which delays him long enough for Pidgeot to rescue her.
* WhatDoYouMeanItWasntMadeOnDrugs: There are some pretty fucked up moments in the story, and whether it's a good or a bad "fucked up" all depends on the reader. As mentioned on the ThisIsYourPremiseOnDrugs page when it still had examples:
---> ''Latias' Journey'' is ''{{Pokemon}}'' tripping balls on every hallucinogen known. On meth. And PCP. And Rare Candies. While huffing nitrous oxide. And off its mood stabilizers.
* WhatDoYouMeanItsNotForKids: Yes, ''Latias' Journey'' is based on the kid-friendly Anime/{{Pokemon}} anime. But it also contains NightmareFuel, intense violence, intense gore, horror, sexual situations, GratuitousRape, profanity, and [[ArsonMurderAndJaywalking philosophical/religious overtones]].
* TheWoobie:
** May. First she gets OvershadowedByAwesome and ditched when Ash has to go solo at the beginning. Her crush on him goes [[UnrequitedLove unrequited]] [[note]](we later find her first crush was too -- he ditched her for a gay zombie.)[[/note]] Then she gets [[CurbstompBattle curbstomped]] and [[BreakThemByTalking insulted]] by a godmoding MarySue. [[spoiler:And when the grand finale kicks in, her Munchlax is shot, Drew's [[YourHeadASplode head explodes in her face]] right as she's realizing her feelings for him, and copies of her parents are killed on public TV. Once she gets an EleventhHourSuperpower with the rest of the cast, [[KansasCityShuffle she's tricked into killing her ''real'' parents thinking ''they're'' copies]], is ostracized by her brother for it, and her Pokemon and eventually herself are slaughtered by [[BrainwashedAndCrazy Latias]] in quite possibly one of the most brutal fatalities of the book.]] ''Holy shit.''
** To a lesser degree, Wobbuffet.

----