Token of Darkness by Amelia Atwater-Rhodes

Cooper Blake doesn't want to remember the accident that changed his life.  No one else wants to mention it.  He doesn't bother with his old friends, now that he has returned to school.  Playing football would be too painful, and hanging out with the team would be too painful in another way.  Ever since Cooper awoke from the accident, he's had a most unusual freind that only he can see - a beautiful girl named Samantha. - and an unusual danger that only he can see - black shadowy beings which are capable of attacking.  Neither Cooper nor Samantha know who she is, or where she came from, or what kind of a ghost she might be... if she really is a ghost, that is.