The S.C. Magi System (マギ) are a trio of supercomputers designed by Dr. Naoko Akagi during her research into bio-computers while at Gehirn. The Magi's 7th generation organic computers were implanted with three differing aspects of Dr. Naoko Akagi's personality using the Personality Transplant OS (Operating System), being her persona as a woman (Casper-Magi 3), her persona as a mother (Balthasar-Magi 2), and her persona as a scientist (Melchior-Magi 1). The same system is used to operate the Evangelions. The Magi are used during Episode 13 to connect the simulation bodies to the Evas in their cages and, presumably, the synch-tests when the pilots are not present in the actual Evas.
There are numerous similarly named systems located in other Nerv facilities around the world including Germany, the United States and China. Each consisting of three separate parts intended to work together. Whether these too are based on the psyche of Naoko Akagi is unknown.
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