AGodAmI AdultFear AfterTheEnd AnachronismStew ArtifactTitle BatmanGambit BerserkButton BigBad BittersweetEnding ChekhovsGun ConservationOfNinjutsu CrazyAwesome CriticalExistenceFailure CurbStompBattle DarkerAndEdgier DidYouJustPunchOutCthulhu DummiedOut EarlyInstallmentWeirdness EldritchAbomination EnemyMine EpicFail EstablishingCharacterMoment FiveManBand GenreSavvy HeroicBSOD KickTheDog LampshadeHanging MagnificentBastard Main MindRape MoralEventHorizon MyGodWhatHaveIDone NiceGuy NoHoldsBarredBeatdown OnlySaneMan OurDragonsAreDifferent PunchClockVillain Recap RunningGag ShipperOnDeck ShoutOut ShownTheirWork SmugSnake TearJerker TheScrappy VitriolicBestBuds WhamLine Woobie YouShallNotPass
has a fairly obvious one. The Godmodder. This isn't completely the case in the second one, where some of the screwiness seems to have a little grounding outside of the Godmodder's influence, but everything in the first game was at least indirectly the Godmodder's fault.
Destroy The Godmodder :
We Are All Pokémon Trainers Missingno, also called The Anomaly and He Who Must Not Be Numbered.
'M in the Unova arc.
Ardos in the Ranger Regions.
Napoleon in the Alternate Timeline.
Annoski during the Keystone arc.
The Master and PEFeDOS during PMD-R.
AU!Alduin in RtAU.
The Ghost Lord in Conquest.
Cipher for Unova-2, Holon, and Orre.
Dr. Rex of . Dino Attack RPG At least, until it gets
Hijacked By Baron Typhonus.