In the episode "The Boy Must Live", September reveals several things:
- At a point in the future, humanity will sacrifice the capacity for emotions for increased intelligence - creating the Observers
- Observers developed techniques for reproducing asexually
- Michael was produced based on September's DNA, technically making him his father
- Michael was born with an abnormality - both Observer-level intelligence and the capacity for emotions, and was to be destroyed
- September decided to hide Michael in the past, to protect him
How Michael ended up specifically where he was in the original timeline is never explained, to the best of my knowledge. That episode indicated he had been alone for some time, so it's likely September broke contact to protect him.