While on the whole an Adventure Game, which allows the allows the player to play through different "Scenarios", where they follow several central characters through several different versions of the plot of the series, the game also has RPG Elements, as well as some Dating Sim, Raising Sim, and even Visual Novel elements.
Most notable about the game is the so-called "Classified Information", which was hyped as a major selling point for the game prior to its release. In practise, the "Classified Information" is a compendium of facts about the universe of Evangelion, which is gradually unlocked during play, and expands quite a bit on the lore of the franchise, especially in many places where the TV series remained silent on the matter. In addition, as the different scenarios shifts to different characters, their perspectives are examined to a much greater detail than in the show, which also fills out some details about lore and character motivations that the show left unstated.
The later part is has caused some controversy in fan circles, as it raises the question of how involved Evangelion's creator, Hideaki Anno, was with the development of the game, and how true to the show's canon the Classified Information should be seen as despite some of the Classified Information being accepted by Studio Gainax as “canon”. According to all official sources, Anno was interviewed "extensively" by the developers and consulted on the game, and the developers also insist that, lore-wise, everything stated in the game should be accurate to Anno's instructions. Anno himself has remained vague on the matter, merely saying that all the information need to understand the story is included within the show, and no additional material is needed.
- And I Must Scream: The visions people suffer from as they're reduced to LCL are hellish and under SEELE's plans they'll be left in this state forever while the villains deify themselves.
- Big Bad: Keel Lorenz, as in the show, is the seldom seen villain but nevertheless Gendō's boss and the one overseeing the Human Instrumentality Plan to make himself a god.
- Dating Sim: The game has some elements of this.
- A Day in the Limelight: Several scenarios puts the player in the shoes of some of the show's less explored characters, such as Asuka, Shinji, and Rei's classmates, as well as the three Bridge Bunnies.
- Dirty Old Man: One of the most infamous scenes from the game is a comedic substory, wherein Fuyutsuki convinces Shinji to dress up as his mother, Yui, much to Shinji's discomfort, and takes pictures of him, when he finds that Shinji really does resemble his mother quite a bit. It undeniably paints Fuyutsuki as quite a bit more of a pervert than in the show.
- Doing In the Wizard: Downplayed. The Classified Information does this to different degrees quite a few concepts which the TV series left more ambiguous in nature, as it traces the supernatural events and artefacts of the show back to the hyper-advanced scientific works of Sufficiently Advanced Alien Precursors (the show at most just vaguely alluded to some sort of Ultraterrestrials being at work). Most notably, it is clarified that the Secret Dead Sea Scrolls are not some kind of divine prophecy, but rather some sort of instruction manual on how the different Seeds of Life work.
- Downer Ending: Depending on the results the player gets it's possible for SEELE to complete Instrumentality as per their designs, leaving everyone else powerless for them to rule over as gods.
- Dragon with an Agenda: As usual Gendō works under SEELE but only so far as their goals align and he betrays them as soon as he gets the chance to begin his own Impact scenario.
- Easter Egg: The Classified Information includes data about a mysterious spaceship found underwater in the Ogasawara islands. This is a reference to Gainax's previous success Nadia: The Secret of Blue Water, where the heroes escaped the final battle in a spaceship they later scuttled in that very place. In fact, Nadia and Evangelion were originally conceived as taking place in the same continuity before Gainax found they could not secure the rights to the former.
- Gay Option: The player is given the option to further Kaworu and Shinji’s relationship in a romantic way. Should the player pick the right options, the player will even have the option to kiss Kaworu as Shinji (other options are embrace or hold hands). Shinji can also confess his love to Kaworu.
- Lighter and Softer: Quite a few of the game's more heavy What If? scenarios are notably much more light-hearted and sillier than the show they are based on.
- Relationship Values: Characters can come to love, like or dislike the player depending on their dialogue choices.
- Ret-Canon: Interestingly, the game is primarily based on the anime TV series, but it also borrows a few elements from Yoshiyuki Sadamoto's official manga adaptation of Evangelion, but tweaks them to better fit in with the anime.
- Video Game Cruelty Potential: Due to the games Relationship Values system, the player is given the option to be a dick to the characters for little to no reason whatsoever.
- What If?: Quite a few of the game's scenarios are this in nature, some of them even taking place in what can be classified as outright Alternate Continuities. Most notably are:
- "Broken Wings": A scenario where Kaworu regains his memories of being Adam, decides to takes his children out away from Earth (including the EVA Units), effectively ending SEELE's plans for Third Impact and the war between Lilith and Adam's progeny.
- "Prudence of the heart": A Day in the Limelight scenario for Toji, which ends in a climax where he fights the Mass Produced Eva Series.