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It seems too simple to say that Otis picked up Sophia and put her in the barn, then got shot by Shane before he could tell anyone . For this to be true, Sophia has to be bitten almost immediately after Rick leaves her. She then has to wander near Otis to be found, and then captured and put in the barn. Based on the tracks Daryl followed, she was heading back to the road, then changed direction. Maybe she ran from a walker, got bit and escaped with her neck bitten. Maybe it was the Walker that Rick and Daryl autopysied?? She runs to the abandoned house and sleeps in the cupboard. The next day she is sick and confused, she tries to cross the river, gets stuck, drops her doll and turns into a walker. Then Otis finds her early in the morning, pulls her free drops her in the barn and then gets back on the hunt in time to bag Carl.
I guess it could have happened something like that, but I kind of got the feeling that Hershel knew who was coming out of the barn next. It would seem more likely that Jimmy (who told Hershel that it happened AGAIN) might have had something to do with it. Maybe he found Zombie Sophia a few days later. He told Herschel, and they decided to put the girl in the barn and not tell Rick. Hershel might have even thought he was saving her from them. This would mean that Daryl was on the right trail. He found where still human Sophie hid for the night (he didn't find blood so it was either someone else, or she wasn't bit yet). He found where she lost her doll (maybe she was bitten by the river). But he doesn't find her. Because she was found stuck in the marsh by Jimmy and thrown in the barn.
Of the two possibilities, I think Jimmy is the more likely suspect than Otis. Maybe I'm just overthinking things, but the later timeline seems to fit the clues better. Maybe there will be a webisode or flashback to give us the real story. Thoughts?