Well, I've hit some major writers block, and combined with some real world events I don't see when I can get the time to continue my virtual third season. So instead of leaving you all hanging, I figured I'd just give a synopsis of where I'd planned to go.
Helen and Lilly continue to investigate Joan's connection with God. Joan finds out, and tells them that it's true. Emboldened by this, she also tells Grace and Adam, but while Grace believes her Adam doesn't, bringing up her lyme disease and solidifying himself on Ryan's side. It turns out Ryan is the son of Lucy Peterson; she's had a lot of plastic surgery and remarried after his birth.
Lucy arrives back in town to keep an eye on Helen and instill some fear in her after Ryan tells her she might be on to him. In the middle of this Will wakes up after a few months and has some subconscious awareness of the things people said to him while he was in the coma. Helen tells him about Richard's visit, and Will finally calls his brother and talks to him, uneasily but still laying a foundation for a better relationship in the future.
It turns out that Ryan is waging a war against all religion; Adam freaks out when he learns about this since his mother was a religious person (not sure if this is another continuity issue, but since I already screwed up and made it AU it doesn't really matter). He comes back to Joan and spills the beans to everyone. In the climax it's Joan's Scooby Gang against Ryan and Lucy in a confrontation inside the school. Price tries to intervene but Lucy pulls a gun and shoots him. In a Return of the Jedi-esque twist, Ryan is shocked as the reality of what he's doing hits him for the first time and turns on her, which leads to both their arrests.
Price lives, but while unconscious he has a talk with God and wakes up a bit nicer than before. The relationships between Will and Helen, Luke and Grace, and Kevin and Lilly are all strengthened, but Joan tells Adam that after everything that's gone on she doesn't see how a relationship can work. They resolve to simply try their best to find a fitting better half at college.