- Annoying Younger Sibling: He has two younger annoying twin sisters, Hikary and Haruhy.
- Apologises a Lot: To Rei, even when compared to canon.
- Cowardly Lion: Even more so than canon, considering the inherently, mind-scramblingly terrifying nature of ENEs.
- Dream Sequence: Shinji has a weird one at the start of chapter 4.
- Eye Scream: When Asherah ripped out one of Unit 01's eyes, Shinji's synch rate was high enough to experience some of the pain (although not enough for any physical injury).
- Has Two Mommies: Shinji was raised by two women (a FSB agent and an Ashcroft sorceress) selected by his father.
- I Don't Know Mortal Kombat: A non-video game variant, where Shinji's skills are strictly attuned to being in the Eva, so he can do nothing but be a punching bag for Toja while in school. His gun training does transfer to the Light Gun Arcade game, but those are designed for scouting potential military recruits anyway.
- Lame Excuse: Shinji admits to himself that finding something to do, anything, in order to delay his visit to Ayanami's place is this.
- No-Holds-Barred Beatdown: On Eshmun.
- Only Clinically Dead: After his first encounter with Mot.
- Only Sane Man: Shinji sees himself as this, what with his constant complaining and lampshading about the ridiculous circumstances in his life. It's not entirely accurate.
- Post-Victory Collapse: After making sure that Rei was okay, he promptly falls asleep from exhaustion.
- Read the Fine Print: Shinji makes sure to read it when joining the training programme, to the irritation of Fuyutsuki.
- Slasher Smile: Shinji, uh, flips out a little bit against Eshmun, the Fourth Harbinger. Just a little bit.
- Strong Family Resemblance: Gendo was hiding it well, but Shinji having Yui's chin made their "recruitment" talk unexpectedly harder for him.
- Training Montage: Shinji's progress from barely moving and doing lots of property damage to normal walking in the EVA.
- Unstoppable Rage: He snapped when he was beaten up by Eshmun.
- Armor-Piercing Slap: Well, more of a punch than a slap.
- Creepy Child: Creepier than canon by far.
- Curtains Match the Window: Part and parcel of her being a sidoci.
- Eye Scream: The one which, in canon was merely injured, was entirely lost in the Unit 00 activation incident.
- Gray Eyes: Both a Type 1 and a Type 2; she both plays into the seer archetype, as well as the cold-distant-and-strong-willed one.
- Naked First Impression: When Shinji meets her for the "first" time, when she is naked in the medical tank and missing one eye. The real (maybe) first time is when she incinerates some hostile operatives Alma-style right before his eyes, which causes Shinji to feel very uneasy everytime he is near her.
- And, naturally, the first time he actually talks to her is the same Naked First Impression as canon.
- No Social Skills: Slightly subverted, as AEE!Gendo didn't dare to neglect Rei like he did in NGE. However, her White nature means that his efforts were mitigated, and she's still cold and distant.
- People Jars: Rei in the medical tank. Wait a moment. A precognitive in a tank filled with orange fluid? Sounds familiar.
- Race Lift: Rei is a sidoci, a white xenomix. This is not so much having her race changed, as having one assigned for once.
- Surprisingly Sudden Death: Rei doing her best Alma impression in her obligatory Book-Ends appearance.
Asuka Langley Souryu
- Ace Pilot: Unfortunately for her, her being only 16 means a lot of restrictions that she feels are detrimental to her piloting.
- Acquired Poison Immunity: See below.
- Conditioned to Accept Horror: As a part of her training, she has gone through Acquired Poison Immunity-styled controlled desensitizing to anything sanity losing.
- Constantly Curious: The 4-year-old Asuka was adorably curious.
- Eye Scream: She lost her eyes by looking at what appears to be a nuclear detonation.
- Flashback Nightmare: Her nightmare about how she lost her original eyes.
- Lamarck Was Right: She inherited a good deal of her mother's genius, who was also genefixed.
- Ace Pilot: According to Ritsuko, she was one of the best pilots of her generation.
- Christmas Cake: Emphasized in Chapter 8 when Toja and Kensuke call her Mrs. Ikari.
- Cloud Cuckoo Lander: Shinji sees Misato as this when they're off duty. Ritsuko ties together an explanation for this and her being a Lethal Chef (see the latter's entry below).
- Drives Like Crazy: As usual, now with her car's interior upgraded with stuff that is better suited for aircraft. (It's a flying car, but still...)
- Electronic Eyes: As standard among mecha pilots.
- Lethal Chef: She has the same sensory issues (and resulting culinary fallout) that she had in ANE. This time around, though, it's due to brain damage caused by exposure to the environment of Leng as opposed to ANE's more directly brutal reason. At least, that's what Ritsuko tells Shinji. It's only part of the truth, and the rest, from her inner dialogue, is best left unspoken.
- Tuck and Cover: She did this to Shinji when the nuke was used against Asherah.