Some information on SUPERNATURAL season six, episode two synopsis:
Sam (Jared Padalecki) investigates a case about missing babies whose parents are being murdered. At one of the crime scenes, he discovers a baby that was left behind and calls Dean (Jensen Ackles) for help. Reluctant to leave Lisa (guest star Cindy Sampson) and Ben (guest star Nicholas Elia), Dean finally agrees to meet Sam and surprises his brother with how parental he has become. The brothers take the baby to Samuel (Mitch Pileggi), who decides to raise it as a hunter, which infuriates Dean. However, before they can decide the baby’s future, a shape-shifter breaks in and attempts to kidnap the baby.
I’m still wondering how on earth they’re going to explain Samuel’s presence since he died at the end of In The Beginning in season four.