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Remember in the first game when Shion claimed to the others about how she got into Vector when she wasn't so smart? Well the only reason she got into Vector was because of her past life as the Maiden, her connection with U-DO and her father was apart of the Zohar Project. I take it that Kevin personally saw to it that Shion was made an employee of Vector Industries by directly showing Wilhelm who Shion was.

Shion was needed in order to retrieve Mary's soul from the U.M.N. and in order to do so, KOS-MOS was created as the vessel in which it would be stored until the time T-elos would come to take Mary's soul into her body, which is Mary's original body. T-elos was programmed to be more malicious and under one thought alone, to kill KOS-MOS. Also, KOS-MOS was merely an observational unit for Wilhelm, Kevin and T-elos until the right time.

Eventually parts of Mary had begun to surface since KOS-MOS' awakening on the Woglinde, and even more so throughout the series. And then finally Mary's true soul surfaced once Shion fully unlocked her inside of KOS-MOS' subconscious domain. I think the entire time throughout the series, Mary was conscious of what was going on around her, but the only time she ever truly acted was when she took over KOS-MOS' body. But in a sense KOS-MOS was Mary the entire time since her awakening on the Woglinde.