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  • Fridge Brilliance:
    • Bill says he's been working on Pokémon Fusion for years. Remember that time he fused himself with a Clefairy?
    • Team Aqua and Team Magma create a fusion of crime syndicates. Also, the game fuses the characters from RSE with the setting of RBYFRLG.
  • Fridge Horror:
    • Elm's lab hasn't been built in New Bark Town yet. Instead, there's a patch of grass where the Chikorita, Cyndaquil, and Totodile families nest. It's not a coincidence that Elm gives out Chikorita, Cyndaquil, and Totodile in Generation IV. He built his lab on top of their home, then captured them to give to trainers.
      • Even more horrifying when you consider what else is under New Bark Town (and hidden by Elm's lab.)
    • There's a cemetery in Goldenrod City and a woman there who says she couldn't stand it if the graves were ever disturbed. Goldenrod City doesn't have a cemetery in Generation IV.
    • Pokémon Fusion, as hinted by Bill at the end of the game, is a sort of fad that no one cares about by Generation IV. When you defeat gym leaders, they hand over their Fusions to you, seemingly disappointed in them ("I guess this thing isn't so great afterall"). When you beat a gym you can even catch Pokémon used by trainers you battled in the gym. Some (but not all) gym leaders and gym trainers abandon their Pokémon Fusions because you defeated them. Not only are you witnessing Pokémon Fusion gradually dying out as a trend over the course of the game, you're causing it!
  • Game-Breaker: Aside from the diverse legendaries you can receive, there's also Gyaranite, which you get from Lance after beating the Elite Four + Champion for the first time. Both of the Pokémon forming it are among the best in the game on their own right, so neither holds the other back significantly. The type combination (Dragon/Water) is extremely powerful, being weak only to Dragon (which it can itself counter) while also coming packed with great offensive power. Because it's a Water-type, it can make good use of important and powerful H Ms (Surf being a little weak due to its focus on Attack over Special Attack, but Waterfall hits like a truck). Also, it looks awesome. There's no real reason not to make it your primary Water Pokémon once you receive it.
  • Les Yay: Janine's crush on the player character (if you're playing as May).
  • Tear Jerker:
    • Mira's farewell to her mother before "leaving" with her Vulpix.
    • Ellie's reunion with her mother.
    • On a meta example, when the game was Screwed by the Lawyers.
  • That One Boss: The Elite Four and Champion are definitely no pushovers, but Lance in particular stands out the first time you face them. Just specializing in the most powerful type of Pokémon in the game is not enough for him. Many of his Pokémon are partially Water (Crocodactl, Gyaranite) or Fire (Chargonite), making the Kill It with Ice strategy usually employed against dragons irrelevant - hope you've got a Dragon of your own fast enough to outspeed his AND powerful enough to One-Hit KO them. His unfused Dragonite is level 60 and has Outrage, so unless you grind a lot, it will likely outspeed most of your party, One-Hit KO almost anything and be tough enough to take hits like nobody's business. After him, the Champion can almost feel like an Anticlimax Boss, especially if you have a Ghost or a Dark type, who will slice through his strongest 'mons like a knife through butter.

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