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Unit-00 is the Prototype, the first successful Evangelion, and is piloted by the First Child, Rei Ayanami. The head design is similar to that of the previous failed attempts, but with only one camera. There are two domes on the top of the head, one white and one transparent green; their function (if any) is never revealed. Unit-00 is the only one of the original Evangelions that is never seen without its armor (Unit-02 was revealed in The End of Evangelion, and Unit-01 on multiple occasions) or opening its mouth; thus the appearance of its organic body is unknown.
Unit-00 was initially colored orange like the previous prototypes, but its armor was damaged beyond repair by the Angel Ramiel's particle beam. The subsequent repairs and upgrades included blue armor plating in addition to other alterations made in order to make it more suitable for combat conditions. It was later refered as Evangelion Unit-00' (エヴァンゲリオン 零号機(改), "Evangerion Zerogōki Kai").
The upgrades to Unit-00's armor make it look more like the subsequent Evangelions, but there are still several differences or actual limitations. Shoulder pylons are added to the Unit's armor; though similar in appearance to the ones on Units 01 and 02, they are used to hold retro-rockets, as seen in the fight with the ninth Angel, Matarael. Because it is only the prototype, Unit-00 cannot be fitted with D-Type Equipment. The true nature of the soul inside Unit-00 is never specified, but it is implied to be directly connected to Rei in some fashion. Unit-00 was self-destructed by Rei in order to destroy the sixteenth Angel, Armisael.
It was damaged during the battle with the fifth Angel, Ramiel, and later repaired and upgraded to the Evangelion Unit-00' (零号機改, "Zerogōki Kai"). It was destroyed during the battle with the sixteenth Angel, Armisael, when Rei activated Unit-00's self-destruct.
Unit-00 plays a very similar role in the manga as it does in the anime. Like its anime counterpart, the manga unit-00 is self destructed by Rei to destroy Armisael.
Since the manga is only black and white, it is unclear if unit-00 is ever repainted from yellow to blue like it was in the anime, the shading on the armor in the black and white panels remains unchanged from its first appearance (shown on the second collection cover to be yellow) and its lighter shading compared to the other units suggests its color to be lighter then the other units which would not be the case if it was recolored from bright yellow to dark blue.
That said, the volume 2 part 2 colored art depicts unit-00, standing with unit-01 and unit-02 along with their pilots, in the recolored dark blue. While the chapter art is not related to the story, it is possible the inclusion was made to signify the change from the yellow to blue color scheme.
In the Neon Genesis Evangelion: ANIMA continuity, after the self-destruction of the unit during the battle against Armisael, its core was preserved and stored in Central Dogma. It was rebuilt using leftover parts from the original Unit-00 and F-Type parts and then repurposed as a specialized sniper unit: the Evangelion Unit-00 Type F.
- "Zerogōki" does not follow the naming system used for the succeeding Evas. Under that system Unit-00 would have been enunciated as "Reigōki" in the series, giving both mecha and pilot (Rei Ayanami) practically the same name.
- Officially the english name is EVA-00 PROTO TYPE, with the word prototype being separated.
- In the Sore o Nasumono: Neon Genesis Evangelion Concept Design Works book, the original designe proposed by Ikuto Yamashita was drastically different from the design used by the TV series, having similar color separation as the design used by Evangelion Unit-00 (Rebuild). It also includes the shoulder pylons and it is mostly yellow, white and gray unlike the one used in the TV series, which is mostly yellow.
- Unit 00's refit design can be seen during the studio scene in Evangelion: 3.0+1.0 Thrice Upon A Time