I think i'm the first to find this. When you go to talk to Kenny in the front of the train, after a few dialog options are 4 dialogue options:
Stop. The. Train.
You're in denial!
This isn't about Duck.
If you are silent, Kenny will speed up the train. The same dialogue appears, if you are silent again Kenny pushes you out the door to the walkway on the side of the train. Lee decides to go back into the box and finds blood all over the ground and bits of flesh and... Clems hat.
Duck turns into a walker and kills everyone, than proceeds to go after Lee, knocking him out of the box car into the brush.
Gave me chills
*Edit* This isn't an alternative storyline. This is just a way to die in the game than it reloads. Didn't mean to confuse.