* CompleteMonster: [[spoiler:[[BigBad Deoxys's]]]] [[EstablishingCharacterMoment first action]] after coming to Earth is murdering and [[ColdBloodedTorture torturing]] a small Pokémon [[WouldHurtAChild child]] after his twin was just murdered before his eyes. Over the course of the story, he [[CardCarryingVillain gleefully]] maims, murders, slaughters, mutilates, {{Mind Rape}}s, 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 [[OmnicidalManiac 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 get in his way. When questioned why he does all of his atrocious acts, he replies thusly:
-->Because it is my wish. Because they were in my way. And most importantly, because I can.
* DarknessInducedAudienceApathy: Besides the sheer amount of over-the-top violence and GratuitousRape scenes, so much crap the heroes get put through makes it difficult to sympathize with them. This wasn't already difficult enough to do so, no thanks to the {{Wangst}} from some characters (mostly Latias, but May is no stranger to it, either, even before anything bad happens to her) and characters like Sadic and '''Mewtwo''' being preachy idiots. Then there is Latias' relationship with the Ghost King, which completely destroys all hope of the main heroine being seen as sympathetic. And there's [[ArsonMurderAndJaywalking Ri2's refusal to]] [[ShowDontTell show and not tell]].
* CriticalResearchFailure:
** Rock-types are NOT immune to electricity. Pikachu could have easily taken both of Latias Sr.'s Pokemon.
** During Crawdaunt's orgy in Chapter 50, Crawdaunt is described as "proud and joyful and omnipresent as any old saturnine god of sex." The author probably meant to say "jovial," because "saturnine" means "sluggish and gloomy."
* 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 Sadic. 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.
** [[TakeAThirdOption Or]], if you loved it at first, you would have a [[HypeBacklash "Why did I think this was good back then?"]] moment when you re-read it to see [[{{Filler}} how]] [[GratuitousRape many]] [[WhatAnIdiot flaws]] this story was rife with.
* 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.]]
* OneTrueThreesome: 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.
* StrangledByTheRedString: The relationship between Latias and [[spoiler:the Ghost King, and by extension, Rayquaza]] is the most disliked aspect of the story. From the very beginning, Latias [[spoiler:has been dreaming about marrying the Ghost King, even though she didn't even know what he looked like. Later on, she forgives the him for razing her hometown and murdering everyone in it in a childish fit of rage, all because because a hologram of Latios said they should get together. She obeys it without question, the reason given that she "just knew" the hologram was the real Latios. At the same time, the Ghost King shows no real remorse over destroying Alto Mare nor killing everyone in it; the only reason he regrets doing it is because it upset Latias. To add insult to injury, their love for one another is mostly [[ShowDontTell told and not shown]] and Latias even marries the damn guy end of the story!]] 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 it little more than glorified StockholmSyndrome.
* WhatAnIdiot:
** The Ghost King wants to apologize to Latias for destroying her city, killing all her friends, and ultimately traumatizing her.\\
'''You'd Expect:''' He'd do everything Pokemonly possible not to dig himself a deeper hole. Wait for her to calm down before sending someone to speak on his behalf, since he can't leave the Realm of Mists. And maybe send a messenger who's not a Ghost-type. Also, drop the bounty on Ash's head, because killing him would just piss her off even more.\\
'''Instead:''' He sends Shedinja, ''the very Pokemon who killed Latias' best friend,'' to hunt her down with a squadron of ghosts and capture her. Oh, and Shedinja is also a {{Jerkass}}, and would rather terrorize her for several days instead of just bringing her right to the King.\\
'''Then:''' Once the King gets to speak to Latias when she has Mewtwo as her bodyguard, he tells her right to her face that he's going to kill Ash anyway, [[HonorBeforeReason because he never breaks his promises]].
** Fearow's gimmick is that he eats other Pokemon and gets stronger from it.\\
'''You'd Expect:''' He'd eat Latias ''immediately'', because she's a legendary Pokemon.\\
'''Instead:''' He tries to [[GratuitousRape rape her for no reason]], which delays him long enough for Pidgeot to rescue her.\\
'''Then:''' He is later killed by Latias' NewPowersAsThePlotDemands - powers that could have been his, had he not screwed around.
* 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 was actually going out with another guy!)[[/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'' demonic fakes]], is ostracized by her brother for it, and her Pokemon and eventually herself are slaughtered by [[BrainwashedAndCrazy Dark Latias]] in quite possibly one of the most brutal fatalities of the book.]] ''Holy shit.''
** To a lesser degree, Wobbuffet. He was abused as a child by his grandfather, and abused as an adult by Jessie. Just when he quits Team Rocket and things are starting look up for him, [[spoiler:Shalor invades Mirage Island and kills almost everyone, including Milotic. Only he and Cacturne make it out alive.]]