WARNING: The following contains spoilers for Evangelion: 3.0+1.01 Thrice Upon a Time, now streaming on Amazon Prime Video.
Audiences first met Mari Illustrious Makinami in Evangelion: 2.0 You Can (Not) Advance, and while some fell in love with her, others were left scratching their heads as to what she added to the story of Evangelion. She was entertaining as the only EVA pilot who actually liked her job, but her character had little bearing on the plot of the second or third Rebuild of Evangelion movies. Mostly, she felt like an extraneous addition included mainly for the sake of fan service. Evangelion: 3.0+1.01 Thrice Upon a Time, however, takes this seeming extraneousness of her character and manages to make her essential to the heart of the story.
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Mari's Role in Evangelion: 3.0+1.01 Thrice Upon a Time
Mari's first major scene in Thrice Upon a Time is, like many of her showcase moments in the previous films, a big battle scene with little direct bearing on the plot. After saving Paris in the opening sequence, Mari disappears from the movie for the next hour or so, which focuses on Shinji, Asuka and a Rei clone living among Third Impact survivors. However, when Mari returns on the Wunder ship, she begins to serve a real narrative purpose. Her flirty interactions with Asuka may be filled with fan service, but she's actually able to mend the rift between Asuka and Shinji, getting them both to confess their complicated feelings. Mari's EVA piloting skills come in handy for the battle against NERV that takes up the second half of the film, combining EVA Unit-08 with other units and keeping up the fight while others are dying.
In the end, though, it's not her EVA piloting that matters most, but her ability to guide Shinji into a universe without EVAs. When Shinji is on the disappearing beach, her presence restores color to his perception. In the movie's final scene, she meets Shinji at a train station, taking his hand as they explore the new world. The implications of Shinji possibly being romantic with Mari might come as a shocker given their lack of interaction throughout the series, but it's that lack of baggage between them that oddly makes her the best dating option for Shinji at the moment. Rei and Asuka have too many psychological issues to deal with, and Kaworu is so intertwined with Shinji's PTSD that they likely need some distance even if they're destined to reunite eventually. Mari represents a fresh start.
The Mysteries of Mari's Past
There is clearly a lot of backstory behind Mari that is never directly explained onscreen. Fuyutsuki calls her "Maria Iscariot," a name that serves as a double Biblical reference to Mary Magdalene and Judas Iscariot. The latter reference implies NERV views her as a traitor. Making matters even weirder is that Gendo's flashback scenes show a woman who looks identical to Mari, if not Mari herself, interacting with the younger Gendo and even introducing him to Mari.
There are two equally likely explanations for this. The first is that Mari is a peer of Gendo, Yui and Fuyutsuki who stayed young for decades due to the LCL-based "curse of the EVA." She clearly knows a lot about LCL, identifying Shinji as a pilot via the smell of LCL, so she might have been the first to experiment. The second possibility is that Mari is a clone. Her family name is Makinami, and given that the Rebuild films explicitly changed Asuka's last name to Shikinami as a parallel to Rei Ayanami and to foreshadow that she's a clone, it would make sense for all three -nami pilots to be clones. Mari might be a clone who still holds memories of her prior incarnations.
Does Mari Represent Moyoco Anno?
One persistent theory/rumor circling the Evangelion fandom is that Mari is meant to represent director Hideaki Anno's wife, the manga-ka Moyoco Anno. It's not hard to see why some might jump to that conclusion; Shinji's journey is so heavily based on Hideaki's emotional state that it makes sense to assume Shinji's love interest would parallel his own. However, Moyoco has denied being the basis for Mari to readers of her paid newsletter, writing, "Please don't compare me to the work any more than you have to. Please don't make me feel uncomfortable about it."
In terms of personality, Moyoco seems to be wildly different from Mari. Moyoco has been very public about struggles with depression that parallel her husband's -- an issue we don't see at all in Mari. However, just because Mari isn't a copy of Moyoco Anno doesn't negate the likely possibility that Hideaki Anno's love for his wife was a general influence on the more romantic mood of Thrice Upon a Time. Sure enough, Moyoco's influence can be seen in the film through multiple cameos of her manga works. The original TV ending of Neon Genesis Evangelion was about Shinji learning to finally love himself. The Rebuild ending expands upon and reworks that message by depicting him learning to love and help others, and Mari is vital to this story arc.
All four Rebuild of Evangelion films are streaming worldwide on Amazon Prime Video.
