My period started on September 24 and ended on September 29 but had brown spotting on September 30. I had unprotected intercourse on the 28, 29, or 30, I don't remember. But then again I had unprotected intercourse on October 2nd and 3rd. All the times we did have sex he came inside me. Could I be pregnant? If so when can I find out the soonest?

Yes you could be pregnant, if you miss your next period, I would try a test then.