I don’t know why, but I seem to have gotten the impression that he abandoned her before BO was born. The whole situation is slightly icky. Imagine her parents. Their beautiful and smart daughter takes up with a Kenyan who is already married, “marries” him (or not), and has a baby in which the father apparently takes no interest. Then she goes off with some guy from Indonesia. It all sounds very unstable, and surely frightening for a little boy. And at the same time, the mother and the grandparents are apparently convincing him that he is the best thing since sliced bread. But to answer your question, I think Obama senior disappeared when he found out she was expecting.
I also believe that he took off when he found out she was pregnant, that is, if he is the father. There is always the possibility that someone else is the father. She may have turned to Obama Sr. because of a scenario in which the real father abandoned her or was unable to marry her because he himself may have been married.