- Rei in the medical tank filled with LCL, by the Word of God, resembles the navigator from Dune.
- Shinji's other foster little sister is named Haruhy.
- Two of Shinji's classmates are aeonized Haruki and Kyonko from Suzumiya Haruhi no Seitenkan.
- The lyrics (heard in Misato's new car) "There are three flowers in a vase. The third of them is..." were a code phrase used to manipulate November.
- "The Hedgehog Can Never Be Buggered at All" is among Nanny Ogg's favorite songs, while simultaneously a reference to Neon Genesis Evangelion's own discussion of the Hedgehog's Dilemma. The TV Show where the statement is made is an Expy of Look Around You.
- 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 ''Use more gun."
- Asuka is stationed in the 2501 Training Facility.
- A lot of Command & Conquer characters work for NEG, with Anton Slavik, Oxnana Kristos and CABAL (as COEUS TITAN) being the most obvious.
- Dr. Sylveste gives young Asuka a Geth as a robotic pet.
- One 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. Translate that from German and all you lack is a song and dance routine.
- Rury may be a reference to 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 A.I.s ("Thank you, Omoikane", "Thank you, COEUS", anyone?).
- APHRODITE And ASPARTAME With APOSTATE.
- Rei gives Shinji the Children of Dune book.
- Japan is referred to as 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 Well Lit Room.
- Unit 03 is being constructed at the 0343 facility.
- The quote for chapter two is from a book by the AEE-universe 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 stand alone events.
Shout Out / Aeon Entelechy Evangelion