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Two things your friend can do. 1. He can fight for custody on this issue, by filing a custody motion with the court. This is assuming that he is named on the birth certificate or has been declared the father through the court. This can be a long process. 2. The other option, and this is a major decision to be made, the state's Child Protective Services can be called and the suspected abuse reported. They will most likely remove the child from the home. They will typically look for a family member, primarily the other parent to keep the child until the allegations are investigated.
Generally, I do not advocated getting social services involved, but sometimes it is the best option. Your friend needs to look out for his son's best interests.
I hope this helps. Please accept my answer and then we can continue this conversation with any followup questions you may have.