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In Evangelion - ANIMA -, Quatre and several other Ayanami clones appear forming an international Anti-Angel hunting task force known as the "Sword of Damocles" network; formed on behalf of NERV with Rei II and Rei No. Trois serving as leaders of the force. The later clones were produced at the same time and have nearly identical figures and appearances with some exception(Rei Six, who is only seven years old). To differentiate them, they were given different hair colors. The fourth clone, Rei Quatre, has silver hair. The Ayanami series clones produced at NERV are said to not develop self-awareness; they are remotely controlled (akin to a reverse of the Dummy System) by the original Rei via a mental link.
She largely acts as Rei II's body when on field operations, whether with the task force or piloting her Unit 0.0 which features a two seated cockpit either with Rei No. Trois or Shinji Ikari (similar to Kaworu Nagisa and Evangelion 13 in Rebuild). Despite claims these new clones lack self awareness two of them develop relationships and one shows signs of a strong personality: Rei Six becomes best friends with Mari (ANIMA), Rei Cinq shows some independence and Rei Quatre develops a close friendship with Shinji though Shinji couldn't tell if this was genuine or due to the mental influence of Rei II.
In Volume 1, the Rei clones are said to begin undergoing a process called "mental contamination" in which they develop self awareness. For Rei Cinq and Rei Six they begin to develop personalities by comparison Rei Quatre goes rogue for initially unknown reasons and forces Shinji and Asuka to search for her.
After defeating the Angel Carrier Type-1 and Type-2, Rei Quatre returns to NERV with the intent to aid Shinji and the rest of the Children against Armaros when it becomes clear that it's far too dangerous to be left alone, for a time.
However, after she, Asuka, and an Evangelion task force established to battle Armaros on the Moon were defeated she suffered a far more intense mind contamination than before along with Rei Six and Rei Cinq. Six and Quatre were crippled by the contamination with Cinq being killed for Armaros viewing her as a threat; being the only Rei clone shown to develop an actual personality in the face of the contamination rather than regress. Rei Quatre began to act independently again(similar to Rei III in The End of Evangelion), immediately shooting Super Evangelion at point-blank range with EVA0.0 [Quatre] and then fleeing, she is later captured by a brainwashed Ryoji Kaji, a loyal leader of SEELE in the ANIMA continuity shown to be the new commander of NERV JAPAN, succeeding Gendo Ikari after his failed Third Impact and Keel Lorenz in SEELE.
She later reappears after her capture by Kaji; verbalizing a deep hatred toward Shinji and repeatedly trying to kill him, yet despite her actions in combat toward him, when Shinji later meets Rei Quatre (still under the effects of the Mind contamination) in person she embraced and kisses Shinji while promising him that she will kill him one day, much to this Shinji's visible confusion and resolute defiance to SEELE.
- Despite it being stated in canon that only the hair of the Rei's is different, they are bodily very different from one another though possessing more or less the same face.
- The fact Rei Ayanami (Rei No. Deux) controls the other Rei's with the help of Rei III(Rei No. Trois) may be a reference and shout out to the fact Ruri Hoshino (popularly called a "Rei-clone") of Martian Successor Nadesico fame controls the eponymous battleship entirely by remote in conjunction with a clone first officer as seen in the film Martian Successor Nadesico: Prince of Darkness
- Her love towards Shinji and mental instability in later volumes may be a reference to the similarly named Four Murasame and Kamille Biden's relationship in the mid to later half of the anime series Mobile Suit Zeta Gundam. Where both Kamille and fellow Gundam Ace Amuro Ray are often depicted to be good friends and mentors to Shinji in the Super Robot Wars video game series.