In the 1st game when they dive to get the real footage of the Woglinde fighting the Gnosis they end up on Old Miltia. Shion sees herself as a child with her father; the last day she saw him alive. From there she ends up in her mothers "hospital" room. We can see her father is dead/ there is blood all over him. There is a blood trail across the room, signs of a struggle. Her mother is in bed covered up to her chin w/ a blanket. There is no sign of movement, but there is no blood on her. It's natural we assume that she is also dead because before even seeing this scene, we knew both of Shion's parents were dead.
When Jin and Shion finally reunite, Shion seems to be upset with her older brother over the death of her parents, as if hould have somehow prevented the tragedy from her memory.
Shion's mother was in an institution implyng that she was either too physically or mentally ill to be cared for at home.
Shion refers to the Miltian Conflict as the time when she lost her parents.

So... we're looking at Old Miltia around the time of the Miltian Conflict. The Song of Nephelim played, the Realians and the URTV's went nuts killing people and wreckin the place up. With the exception of Guinann and Jr., the URTV's were contaminated. Shion's father was visiting the mother alone, possably while the Song played. What if it was her mother that killed her father, a reaction to the Song. Maybe Shion is thinking that if Jin had been taking care of her parents durring the conflict (as opposed to scarring Marg's face up) he could have stopped her mother.
Shion has an extrodinary reaction to Gnosis, was even touched by one and she was fine. Nephelim appears to her on the Woglinde courtesy of the Zohar emulator. She guides Shion through the dive and leads them all to KOS MOS so they can get the data they need. Nephelim tells Shion she has been waiting a long time to talk to her etc. Shion's abilities arent exactly normal, so where did she get them from?

ah.. so maybe shion's mother is a URTV? there were over 600 of them and with jr, albedo and gainun being some of the latest ones it would make sense that they were so young.. maybe shion's mom was one of the earlier models? didn't citrine say they had to have female URTVs to ensure they don't die off? interesting..

It's up in the air still. She could be a URTV, a Realian, an experimantal human* or just a "sick" human. Her being institutionalized just makes me suspicious :look:

*Mary and Shelly are experimental humans that were owned illegally by a pharmaceutical co. Jr and Gaignun took them in 12 years ago.