I work in this area, although I'm not a social worker.
Yes, SS will become involved.
There will probably be meetings to discuss the risk to your children. You, your partner and your children's father will be invited to some of these meetings, so yes he will be involved. Professionals are also invited to these meetings such as a school teacher, GP and a probation worker.
There could also be meetings that are only for professionals such as your children's SW, school teacher and your partner's probation/support worker. I'm these meetings they will openly and honestly discuss the risk to the children and any solution they seem necessary.
In short, to answer your question, yes. Your children's father and school and any other professional SS think should be informed will be told.
If SS think the risk to the children are high enough they will give you a choice. Seeing your partner (even if he doesn't live with you and you say you never allow him around your child) or your child. Think very carefully about your decision moving forward.