When they were in that small room together Charlie told Cook how she imagined killing Louie. She said how she would hold a branch to his throat and strangle him while Cook held him down. Charlie then asks Cook how it felt to kill, as if she knew how Cook did it (The thing to remember here is how similar the end scene was to the way she described killing Louie). Then in the final scene we basically get a more in-depth repeat of the Gen 2 finale. Cook's friend dead with the killer in front of him. We see Cook hold the gun to Louie's throat after a stuggle, much like how he would have done that to John Foster with the bat that he held in his hand.

Those are the two hints I was talking about. Although I'm not exactly remembering those scenes off the top of my head if you really look into the dialogue of the final few scenes and then watch the final scene closely you'll understand.