* In ''Eva'' fanfiction, the PeggySue fic is ''extremely'' common, the most well-known being the doujin ''Manga/ReTake'' (which, in a suitably ''Eva'' way, is actually [[spoiler:a subversion]]). There are also fics out there that set up a ForWantOfANail situation, and then reveal that either the changes were actually caused by a PeggySue or some type of EternalRecurrence situation. There are also {{Crossover}} fanfics with a PeggySue. It's reached the point where [[EpilepticTrees some fans think that]] ''Anime/RebuildOfEvangelion'' is one of these!
* [[AfterTheEnd Post-Third Impact]] fic. This can range from Shinji and Asuka by themselves in a wasteland, to everyone coming BackFromTheDead and the world returned to (mostly) normal. Most of the time, Rei has vanished and Toji gets his leg back (both of which might be supported by canon).
* [[invoked]] There is a mini-genre of ''Evangelion'' {{Fix Fic}}s that work by making the setting CrazyAwesome. This was [[TropeMaker started by]] ''FanFic/ShinjiAndWarhammer40K'' and continued by ''FanFic/NobodyDies'' and ''FanFic/MobileFighterEvangelion''. The controversial ''FanFic/NeonExodusEvangelion'' might be considered an UrExample. Some people thought Rebuild was an official version... [[spoiler:[[DarkerAndEdgier until 3.0 came into the picture]].]]
* There have been several stories involving Shinji being raised by someone other than his uncle/teacher and exploring the ForWantOfANail aspect of how Shinji's personality changes. Sometimes Shinji gets raised on a product, like the aforementioned ''Shinji And Warhammer 40K''.
* Reincarnation fics, especially Kaworu/Shinji ReincarnationRomance. As well as explaining how the different canon continuities are related to each other, this gets rid of the pesky "Kaworu [[spoiler:is an Angel]]" problem and lets poor Shinji be happy for once. They are especially popular since the third movie of ''Anime/RebuildOfEvangelion''.