Ash's Return

"Make a Pokémon that defeats all Pokémon other than Pokémon that defeat themselves!"

"All his life, Ash has had a dream: to Catch 'Em All. And now, he's finally done it– or has he? What mystery awaits him on Cinnabar's shore? And is he ready for where it will take him?"

—the summary

Ash's Return is a short Pokémon fanfic by "Questionnaire," following our hero Ash's quest to find the mysterious "missing" Pokémon. Flavors of Godel Escher Bach and Inception, with bits of "bored in Computation Structures class."

It can be read here. There is also a rewritten version, currently incomplete.

Tropes used in Ash's Return include:

Alien Geometries: The strangely-connecting doors in the "city."
Ascended Glitch / Eldritch Abomination: Missingno itself.
Bavarian Fire Drill: part of the "plan" in Chapter 3.
Cheshire Cat Grin: "Meowth making a large, toothy, lopsided grin."
Discontinuity: "We all know there are 150 Pokémon, and Mewtwo is the last" (says the one who owned a Togepi in the anime)
Divide by Zero / Logic Bomb: the page quote at the top.
Exposition: Chapter 2 is pretty much just this.
Foreshadowing: "Wouldn't want anyone to get hurt, y'know?" and various less blatant examples.
Go Mad From the Revelation: What happened to Professor Vattha.
Gratuitous Japanese: Getto da ze! Dokokashira?
Laser-Guided Amnesia: "I don't remember anything."
Load-Bearing Boss: invoked explicitly by name.
Ontological Mystery, The All-Concealing "I": The italicized portions at the beginning of the chapters.
Painting the Medium: Chapter 3 ("Parallel Process") uses three columns of text to represent three simultaneous lines of action. Until...
Shout-Out: The chapter titles are all references to some computer-science concept. The keys are named after the axioms of ZFC set theory.
So What Do We Do Now?: the beginning, actually.
Team Rocket Wins