The Maiden
"In the distant past, she laughed and cried together with you. She is your other half." - Nephilim
Shion's consciousness has existed in the universe since the era of Lost Jerusalem; when she shared a close relationship with Mary Magdalene as the Maiden of Mary. The brief memory she saw concerning Mary and Yeshua prior to KOS-MOS's awakening was not a product of KOS-MOS's memory, but her own.
In the ancient era of Lost Jerusalem, there were 12 people who served as Apostles to the man referred to as the Messiah. In addition to the Apostles, there were numerous other's around the Messiah, as well. Among these other people, was Mary-- whom is called the Partner of the Messiah.
In order for Mary to use her power of Animus, there was another person who served as her Apostle-- the Maiden of Mary; Shion's previous existance. The Maiden was in constant company of Mary in the same way the Messiah's Apostles accompanied him.
The Maiden served as the key that allowed Mary's power of Animus to be released. Thus, before the power of Animus could be manifested, both the Maiden and Mary were required.
However, sometime between the release of this power, and Mary's own death, the Maiden met with death. When Mary's consciousness awoke within KOS-MOS, she expressed regret over the fact that she hadn't been able to protect the Maiden. Considering this, it can be assumed that, after Yeshua's power of Anima had been divided, Mary lost her power of Animus. During this time, the Maiden died, and Mary had been unable to do anything.