Now, as for my feelings. I think Sophie either:
1. Has healing powers because she's preggo w/Ben's child
2. Is something "else."
I'm tending to lead toward the idea that she's something else. She IS the Omega, meaning she's the last. I think this is the case because she is pregnant with Ben's child and now brings both bloodlines together.
I don't know about Jonesy. I think she killed him to save Brother Justin. How did she know Justin was shot? Well, she's got some pretty damn amazing powers, so why wouldn't she know? Ben "heals" and Justin "Feels." It's always been that way. She could just be gaining that insight from her pa. She also wasn't terribly suprised to see Justin laying there covered in blood.
So, she may have used Jonesy to heal Brother Justin. If that is the case, then it's possible that Jonesy's spirit / personality may start to come through in Brother Justin (the same way Lodz came through Ruthie.)
Now, my heart tells me Jonesy isn't dead. I think people who have been touched by Avatars (either of light or dark) are forever changed.
First off, we have Lodz. He had the powers of empathy. Actually, if you read his profile, it was Scudder who gave him these powers, but the price was his sight.
Second, you have Ruthie. She was resurrected by Ben, using Lodz' life. She now has one foot in the spirit world and one foot out.
Third, you have Appy. She was raped by Brother Justin and went into a catatonic state after Sophie was born. Justin also had sex with various women, all of whom were "not the same" after he was finished with them. Appy had the gifts of telekenisis and perhaps the gift of prophecy, though I tend to think that came more from Sophie than from Appy.
All of that said, it appears that once a person is healed, touched, altered by either a Creature of Light or Creature of Darkness, they are changed. I'm hoping that Jonesy will survive because he was healed by Ben, that he will simply be stronger and can make it through.
If Sophie healed Brother Justin, it could very well be that she used Stroud to do it instead of Jonesy.
One thing that did catch my eye in season 2, was when Sophie gave Ben another tarot card reading. The Lovers appeared and Sophie and Ben both had visions of kissing one another in the field where the bomb went off. The odd thing? Sophie was wearing Jonesy's baseball mitt. Just have to wonder if that's a sign he really is dead. Jonesy also said something to himself (muttered) "when you were little, you used to think the hems were veins." He said this while Sophie was doing hard labor and he was staring down at his mitt. He then rolled the baseball to her and walked away.
According to Sophie's profile (and Jonesy's) Sophie was kind of a pest when she was little, following Jonesy around everywhere and idolizing him. He taught her baseball, etc. So, if she did truly kill Jonesy, she's going to end up really regretting it.
This leads me to my second train of thought (er.. or is that like my 6th or 7th train of thought, anyway.) I think Sophie was possessed or that there may really be two personalities struggling within her. Remember when she was in the shack and she was shown her mother being raped by Justin? She's approached by the figure in the veil (who turns out to be Sophie herself.)
Every prophet in her house.
"This IS YOUR house," she tells Sophie. Then we hear Sophie scream. Something happened to her, against her will. Perhaps she went mad, or, the "other personality / other Sophie" came forth.
I have more, but won't bog down this post. Will post below. Hahah. Sorry, I'm a GEEK!
