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I believe that I can help you with this situation.
I believe that the best time to tell him something about his father is when he starts asking serious question. Until now he does not seem to think about his father nor does he yet understand about procreation.
When he does ask you can limit the details to his understanding of what is involved in making a baby.
If you have God in your family then you can tell him that God wanted you to have a wonderful boy and this is what you prayed for. You had expected to get married but some man came alone and made you pregnant and you had him as your beloved baby boy. He is the answer to your prayers and the absolute joy of your life.
This story is positive, it leaves out the violent and unwelcome nature of the attack and portrays it as a fulfillment of your deepest desire - to have a baby boy. This is true, in hindsight, but it will initially introduce him to the most positive aspect of what was then a most fearful and intrusive experience.
Tell him you don't know the man and were scared at the time, if he wants to know more detail, but that afterwards you were joyful and give thanks for the wonderful gift that you received.
You don't have to invoke God, but other entities such as good fortune, your guardian angel, or whatever way fits into your personal family culture and convictions..
All will be fine. You are such a loving mother that he will always read the benefits of having you as his mother.
He also has a good male role model, and so his development will be unimpeded and perhaps better because of your parents in his life as well.
I shall keep you all in my prayers.
Do not worry about this. All will be well.
Elliott, MAE, LPCC, NCC, CCMHC