A secretive and powerful government agency fights off Alien Invaders with poorly understood technology (which in reality is just derivative of the aliens' own tech). The aliens possess strange forms and esoteric abilities, and are only defeated by the involvement of Ordinary Highschool Students.
The main characters correspond quite well to the characters of NGE, with the exception of the main character, and to a degree Jungo Torii. Curiously, the only NGE main character not to have a direct equivalent is Rei Ayanami. Most of the social dynamics prevalent in NGE apply just as well, with some obvious differences such as the lack of actual familial bonds between the Ikari expies (they're mostly reduced to coworkership) and the strong bonds the Protagonist strives to forge with everyone to brave the oncoming storm rather than the isolation themes enforced in Eva.
- The Protagonist is a charismatic leader who, depending on choices made, is a powerful force that can easily assemble teams capable of challenging destiny and convincing enemy leaders to join under his banner or ensure a faction's victory merely by lending his assistance. This alone marks him as a unique character unrelated to NGE dynamics, though both the manga and the anime have him directly contrast Shinji Ikari's "I mustn't run away" with "I can't run away".
- Daichi Shijima is Shinji Ikari. Uncertain and cowardly, he has difficulty accepting the circumstances that he finds himself in and his immediate reaction to danger is to try and run away. Eventually undergoes Character Development, but is widely disliked by the fanbase. He is an everyman thrust into the extraordinary, and represents the audience (which may factor in to why he is disliked). He also tends to muse on the situation he finds himself in and comes to depend heavily in the protagonist until he finds his own reasons to fight.
- Io Nitta is also Shinji Ikari, at least in how she deals with confrontation. Her policy is to agree with everyone whenever possible and immediately apologize whenever someone takes offense or disagrees with her. This is made even more clear when Airi Ban, the Asuka counterpart, criticizes Io for her constant apologies. Additionally Io watched her mother die in front of her. Her weak will makes her vulnerable to requests, and she puts others' needs before hers, which is why she decides to join the Protagonist in JP's in the manga.
- Makoto Sako is Misato Katsuragi. She is dedicated to the organization that took her in after the accident that left her scarred despite growing dissatisfaction with its policies and leadership. She is compassionate for the plight of the civilians, but puts the assignments first. She may have a crush on the main character.
- Yamato Hotsuin is Gendo Ikari. Cold and dispassionate, he leads the last line of defense against the alien threat with an iron fist. He sees his subordinates as pawns and although he has no compunction with sacrificing them for to reach his objectives, he is nevertheless respected for his iron will and leadership. He knows far more about the situation than he lets on, and a secret plan for the aftermath that could reshape the world. This also makes him embody SEELE's Ancient Conspiracy roots and ruthless, dogmatic ideology.
- Airi Ban represents Asuka Langley Soryu, in both appearance and personality. Red-headed and fiery-tempered, she has problems expressing her true feelings and often rushes ahead without thinking of the consequences. She is deeply self-conscious, butting heads with others when they fail to meet her standards. She is unable to let go of her past, despite her attempts to become more flexible in order to fit in better in the new world she has been drawn into.
- Hinako Kujou is Mari Illustrious Makinami. She has great skill and a lot of enthusiasm but has a tendency to rush in and her stats encourage slugging it out with the enemy. Her relationship with the main character is a pretty friendly one. Also she shows a lot of skin. She has a mostly comical rivalry with Airi and an eminently happy-go-lucky attitude.
- Keita Wakui and Jungo Torii are Touji Suzuhara. Keita is the tough Osakan one who argues with the other characters and is (initially) unfriendly to the main character. Jungo is the strong, friendly one who might also reference how slow Touji is exaggerated as in fanfics.
- Fumi Kanno is Ritsuko Akagi. She's a bit cold but has a friendly relationship with Makoto and teases her about her closeness to the main character. She also decides to side (at least initially) with Yamato over the others. She is profoundly disinterested in dealing with other people and ignores morals and common sense when immersed in her research.
- Otome Yanagiya is Yui Ikari, as a softer, more compassionate scientist than Fumi, though she is very distant from her adopted daughter Koharu, despite the fact she profoundly loves her. She is the Team Mom for JP's and the team doctor.
- Both Ronaldo Kuriki and Yuzuru Akie are Ryoji Kaji, albeit different aspects of the man. Dera-Deka also has parts of him as well. To wit, Ronaldo and Dera-Deka are seeking the truth of the Septentrion invasion, and Dera-Deka (Airi's father) dies for it. Dera-Deka attempts to serve as a mentor of sorts to the Protagonist and often offers worldly advice. Ronaldo is not averse to sharing information and conversing even if you are technically in opposite sides. Yuzuru, or "Joe" is the lazy, irresponsible facade hiding Hidden Depths.
- The Anguished One is Kaworu Nagisa. One of the enemies in human form? Check. Can be convinced to stop the system and put the fate of the world in the hands of the humanity? Check. Has some subtext with the main character? Check. Links to the local Ancient Conspiracy and to the man who could derail the entire trial to pursue his own agenda? Check.
The Liberator Ending is also pretty much a reference to the original Gainax Ending, with most of the world destroyed and only a tiny bastion of Humanity left.
Conversely, this also explains much of why the anime was not well received: while the use of tropes like Anyone Can Die is fairly bold, overuse from attempting to compress the fairly complex story in only thirteen episodes led to Darkness-Induced Audience Apathy. The extreme compression of the plot and the consequent focus on the MC, Yamato and the Anguished One changed the message of the game from "a lone soul cannot hope to fully embody humanity; one needs others if one wishes not to be alone" to the exact opposite. The original game was a love letter to Neon Genesis Evangelion. The anime attempted to emulate the impact Eva left and ended up feeling more like a shallow imitation.