this is a fairly complicated situation, and I am not sure there is a clear 'best' path to follow. I too believe that the truth has a way of sneaking out in some form or another, so best to be in control of how your son hears it. It sounds as if your son has an attachment to the man he believes to be his father (let me refer to him as Dad). You should deal with that relationship exactly as you would if he was the bio-dad, because that is your son's father figure. Let me first write about managing that relationship.
The first concern is for your son's safety and wellness. If you have serious concerns that spending time with Dad places your son at risk, than you need to seek legal advice for how to protect him. If you have less serious concerns, perhaps that your ex is not exactly the person you want spending time with your son but is not going to harm him, then you should help your son maintain the relationship in whatever form he (your son) is most comfortable with. Even a less than perfect father can be a critical factor in your son's development. A father's love is nothing to take from a child unless you have very good reason for believing it will be harmful to your son. Boys without father figures often struggle with anger, feelings of rejection, and confusion about what it means to be a man. If you can protect their relationship without jeopardizing your son's well being, you should do so. If your son expresses worries or unhappiness about spending time with his father, however, he should be free to make up his own mind about that.
With regards to bio-dad, your son will have a right to the truth, but perhaps not at this time in his life. Unless you have some reason to believe that the truth will come out soon, you may want to think about waiting until your son is older, say perhaps 14 or so, to bring this up. I think if you have the ability to wait, it might be best to defer until your son is more mature. Your typical 9 year old would have a hard time understanding the mechanics of paternity, fertility, and conception and all of that, never mind that you would have some pretty awkward explaining to do about why there was confusion in the first place. Nine year olds tend to have trouble taking someone else's perspective, so he would not really be able to 'get' the whole situation with regards to why you made the choices you did.
Once your son is a bit older, he may be able to appreciate and understand why you chose not to share the information. An adolescent is more capable of thinking in terms of weighing options and predicting consequences than a 9 year old (9-10 year olds tend to see the world in pretty black and white terms, with little room for abstract reasoning). A young teen should be able to have some understanding that decisions can be hard to make, and be able to have some ability to see your point of view. When you tell him, it will be important to be matter of fact about the type of things his biodad does or has done, and why you did not feel that he should be part of your son's life during his childhood. You don't need to go into detail, but very matter of fact. Short explanations like "He used to drink a lot and have trouble controlling his temper" or "He hit me and I was afraid he might hit you too" will do fine. Do not vilify the man, because your son will need to hear something positive about him too (even a small thing will mean a lot, most people are not 100% good or evil). Be prepared that your son may want to meet his biodad, and consider if you (and biodad) can allow that to happen. It probably will mean a lot to your son that his father wanted to be able to raise him, even if he was not actually able to be the dad your son deserved to have.
Hearing the news is likely to be very unsettling for your son and perhaps your daughter as well. If your son has trouble adjusting to the news, seek family therapy with a psychologist. Your pediatrician or primary care doctor should be able to recommend someone skilled in helping families through rough spots. This would be a wise step to take regardless of how well your son appears to tolerate the news, as teens can be unpredictable when emotional.
The book 'Questions Kids Ask and Are Afraid to Ask About Divorce' is a great resource that will teach you how to have these difficult discussions.
Best of luck to you.
Disclaimer: This post was written for informational purposes only. It is never intended to replace face to face psychiatric, medical or psychological care. This post is not intended to create a patient-clinician relationship, or to give or rule-out a diagnosis.
I was 14 when I found out that my "dad" wasn't my "real dad". My parents didn't tell me, I found out on my own and was absolutely furious. 16 years later, I'm not furious anymore.....just fustrated. I spent alot of time searching for my biological father because no matter what my mother told me, I needed to find out the truth about him for myself. I eventually found him....he actually lives about 2 miles down the road and I never see or speak to him because that is my choice.
The fustrated part? Because when I go to a doctor and am asked my family's medical history.....or when I fill in a family medical history for one of my children.....things get more complicated when I have to answer "I have no information about my biological fathers side of the family" which makes thier jobs harder. That is one reason why he should know....if for nothing more than healthcare.
As far as telling him? I, from personal experience, think you should tell him. What age is the right age? There is no number that is the right one....but his maturity level....when he's ready, you'll know. Reading your story and looking back at my personal experience, I wish my mother had sat me down, with BOTH of my fathers and calmly explained everything to me. It would have saved alot of anger, fustration and feelings of betrayal. He will probably experience all those feelings and more, but he may not.
Rest assured though, he is going to have alot of questions about the whole situation....you and his bio-dad; you and his dad; how you found out; what's his bio-dad like.....curiosity which is all normal. Hope this helps dear.
This is a complicated situation to handle with, but I think it will be better if your son knows the truth after he gains proper maturity to understand the situation.