Mari Makinami is by far the most controversial element of the Rebuild saga— and in many cases, rightfully so.
From day one, Mari seemed to exist solely as the "aggressive pilot with big boobs." Her character did little to advance the plot, and she lacked a certain depth that both Asuka and Rei contributed to the show.
Given that Mari wasn't a part of the original manga or series, most people felt her existence was entirely irrelevant to the movies. And it seemed accurate enough for most of the saga; until the ending of 3.0+1.0: Thrice Upon A Time shocked us by making her Shinji's endgame.
Why would Shinji end up with Mari and not Asuka or Rei? Was Mari's character really as lacking as we'd made it out to be?
Mari's Unnoticed Role In The Rebuild Saga
Creator Hideaki Anno admitted that Mari wasn't his idea and added her only after a request from one of the producers. However, this doesn't entirely diminish Mari's importance as a character.
The point of Mari's character was to help the main cast develop. Being the only one among them without major psychological issues, Mari played the role of the person that helped Shinji and Asuka come to terms with their emotions and trauma.
It was Mari who urged Asuka and Shinji to untangle their complicated feelings towards each other. She constantly helped the characters develop and progress, and in a way, she existed partially to help them gain a grip on themselves.
Essentially, she became the light-hearted, thrill-driven character that supported the characters like a plot device.
Apart from that, Mari was also meant to act like a tool to destabilize the plot and prevent it from being the exact same as the series.
According to Anno, Mari was thrown into the movie as an extreme foreign element to help deviate the film's plot from the series. The presence of a third female pilot created an opening to do something new with the Evangelion story. Though Anno struggled with Mari's character, he decided to wing it as the movies progressed.
This explains why Mari's character felt so forced in the first few movies. She was shoved poorly into a story that did not seem to require her, and there was barely any material for fans to build a connection with her on.
However, by the time 3.0+1.0: Thrice Upon A Time came out, it looked like Anno found the essence of the character Mari was supposed to be.
Why Did Shinji End Up With Mari?
At first glance, it doesn't make sense that Shinji ended up with Mari instead of Rei or Asuka. But if you let the thought settle, there does seem to be a reason behind the odd pairing.
Shinji ended up with Mari because she was the fresh start he needed.
While both Rei and Asuka symbolized Shinji's need to run back to comfort or throw himself into work (respectively), Mari symbolized his growth from a traumatized young boy to a stable adult.
Think about it: Shinji's biggest fear was socializing and human connection, much like his father. For most of the show, he was the young boy who preferred the comfort of the things he knew and never voluntarily ventured out into the unknown or strange.
After all the hell he'd been through, being with Mari was symbolic of his growth into a young adult who was learning how to connect with people, no matter how strange or unknown they seemed to him.
There's still the argument about Shinji and Mari's relationship not being developed enough. It's important to note that we saw them together as adults — which means they had enough time to get to know each other and grow into a relationship.
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The Reason Asuka And Rei Didn't End Up With Shinji
Asuka and Rei are some of the most well-written and amazingly fleshed-out characters in the Evangelion series. They aren't female leads created for the sake of fan service. Both of them are 3D characters with their own past, personalities, and motives, which makes them so much more memorable on their own.
But ending up with Shinji would've reduced Asuka or Rei into a love interest. Anno likely didn't want that, which is why instead of focusing on pairing the characters with someone, he let the movies end with the spotlight still on them individually.
This disappointed more than half of the NGE fandom, but ultimately, it's a choice to respect.
Besides, if Shinji had been with Rei, it would've paralleled his tendency to run back into his mother's arms, since Rei was both literally and symbolically a clone of Yui.
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And in the Rebuild series, it was made quite clear that while Asuka and Shinji might've had feelings for each other at one point, their hatred and disgust was much, much stronger. This wouldn't have made it possible for either of them to be happy together.
In fact, with either of these characters, Shinji would've ended up in a pretty toxic relationship. Mari was his chance at a healthy, normal, not messed up relationship.