I live in VA.My husband and I have lived in separate parts of the house for over 2yrs.In July I slept with someone and find myself pregnant. We have a 6yrs old son. I'm scared to tell him for I know he will try to take my son away from me. The father of the baby lives out of state. Can I leave to go home and have this baby and take my son with me?

No. This is his son too, if you try to leave he can force you to return or you could lose custody.

Just having relations with another man when you have, essentially, been living apart will not be enough to get him custody. Also, if you are still married when the child is born, he will be presumed the legal father.