Stefano’s comments while he was talking with Hope. Both John and Hope were held captive by Stephano at one point, could they be the biological parents? Stefano warned Hope that if her grandmother didn’t want her to know, maybe there was a reason? Maybe by the time Alice found out, it would have ruined two of her favorite people’s (John and Hope) lives? Stefano would love to raise a child with both Dimera and Horton DNA!
Or the child is Princess Gina and John’s biological child? Princess Gina was crazy in the end but we don’t know much about her life before that point other than John was supposedly involved in it. Maybe Stefano was willing to risk the maddess to get the potential brilliance of John’s DNA?
Also, the potential for conflict within EJ when he finds out John is his father and he has condemned his own father to prison for what he did.