Marduk Institute

The Marduk Institute (マルドゥック機関, MARUDUKKU Kikan) is, supposedly, the secret selection committee that screens the global population for 14 year old children who would make suitable Evangelion pilots.

However, Ryoji Kaji's investigations in Episode 15 reveal that the Marduk Institute does not really exist; it is a dummy organization composed of 108 front companies, and Eva pilots are actually hand-picked by Nerv. All potential Eva pilots are then transfered to Class 2-A in Tokyo-3, to keep them safe and on-hand should Nerv require them.

The factors for selection are unclear, as is the selection process itself. Whether Ritsuko alone picks the candidates (with or without consulting Gendo), or if Gendo and Ritsuko are involved together remains unanswered. Since Fuyutsuki and Chairman Keel are listed on the board of directors of the phantom companies, they might have a (limited) degree of involvement as well, or at least know the truth about the Marduk Institute.

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In Episode 04 Gendo tells Ritsuko that "According to the Marduk Institute's report, the 4th Children has yet to be found."

Moreover, in this scene Gendo and Ritsuko are just talking to each other (albeit with Rei standing with them).  Gendo and Ritsuko are fully aware of the true nature of selecting Eva pilots, thus when essentially in "private" (with only Rei to hear them) it should probably be assumed that they were saying the truth.  Thus, has the "Fourth Children" actually not been "determined" yet?  Eventually, Toji Suzuhara is "selected" as the Fourth Child in Episode 17, but his "selection" is shown to be a sham.  The overall question is:  did Gendo and Ritsuko honestly not know which of Shinji's classmates would be selected as the next pilot this early in the series, or was he selected to be the Fourth Children years before the events of the series begin?  Shinji synchronizes with Eva 01 because his mother Yui's soul is in it, and Asuka synchronizes with Eva 02 because her mother Kyoko's soul is in it.  It takes years to build Evangelion Units.  At what point is an Evangelion Unit imbued with a human soul?  Do they select the most suitable pilot and then use the corresponding soul, or vice-versa?  

Notes

• The "Marduk Institute" is really 108 front companies: this might be yet another religious reference, as there are 108 sins in Tibetan Buddhism, and 108 beads on a Hindu or Buddhist rosary, with a separate head bead.
  • In Buddhism, 108 is also the number of steps or earthly temptations that a man must overcome to attain Nirvana.
  • In Hinduism, several powerful Gods and Goddesses have 108 names. In this case, all 108 different names are merely aliases for a single organization: Nerv itself. The Babylonian God Marduk, after whom the organization is named, had fifty names himself.
• In Babylonian Mythology, Marduk was the God who created humans to bear the burdens of life so that the Gods could be at leisure.