* Rei in the medical tank filled with LCL, by the WordOfGod, resembles the navigator from ''{{Dune}}''.
* Shinji's other foster little sister is named [[LightNovel/HaruhiSuzumiya Haruhy]].
* Two of Shinji's classmates are aeonized Haruki and Kyonko from ''FanFic/SuzumiyaHaruhiNoSeitenkan''.
* The lyrics (heard in Misato's new car) ''[[{{Dollhouse}} "There are three flowers in a vase. The third of them is..."]]'' were a code phrase used to [[LetsGetDangerous manipulate]] [[{{Dollhouse}} November]].
* ''"The Hedgehog Can Never Be Buggered at All"'' is among [[Literature/{{Discworld}} Nanny Ogg's]] favorite songs, while simultaneously a reference to Anime/NeonGenesisEvangelion's own discussion of the Hedgehog's Dilemma. The TV Show where the statement is made is an Expy of LookAroundYou.
* The narrator notes that while regular firepower doesn't do much damage against the Angels, a viable option in the event of failure would be to ''[[VideoGame/TeamFortress2 Use more gun]]."
* Asuka is stationed in the [[Franchise/GhostInTheShell 2501]] Training Facility.
* A lot of ''CommandAndConquer'' characters work for NEG, with Anton Slavik, Oxnana Kristos and CABAL (as COEUS TITAN) being the most obvious.
* Dr. Sylveste gives young Asuka a [[Franchise/MassEffect Geth]] as a robotic pet.
* One [[Series/{{Firefly}} Doctor Tam]] has been assigned to Project Evangelion after a "nasty family related incident". No good can come of this if River happens to get involved.
* Dr Schauderhaft and his subordinate Feucht. [[BilingualBonus Translate that]] from German and [[WebVideo/DoctorHorriblesSingAlongBlog all you lack is a song and dance routine]].
* Rury may be a reference to [[MartianSuccessorNadesico Ruri Hoshino]], both sharing her name (in a suitably Nazzadi-altered form), being a product of genetic manipulation and displaying a tendency to thank their AIs ("Thank you, Omoikane", "Thank you, COEUS", anyone?).
* ''[[Anime/PantyAndStockingWithGarterbelt APHRODITE And ASPARTAME With APOSTATE]]''.
* Rei gives Shinji the ''[[{{Dune}} Children of Dune]]'' book.
* Japan is referred to as [[Anime/CodeGeass Region 11]].
* The room used to house 01 is designed so that there are absolutely no shadows anywhere inside. In other words, it's a [[AlanWake Well Lit Room.]]
* Unit 03 is being constructed at the [[{{Halo}} 0343]] facility.
* The quote for chapter two is from a book by the AEE-universe [[AlphaCentauri Sheng-ji Yang]].
** And for chapter 16, Pravin Lal.
* Cult activity increases with the appearance of Mot. The Office of Special Services classifies these as [[GhostInTheShellStandAloneComplex stand alone]] events.
----
<<|ShoutOut|>>