The question was asked Where do atheists believe the baby’s soul comes from? I am unsure if any theist knows what a soul is. They use words without identifying what the words mean to them. Most often they don’t seem to have a clue.
I as an atheist think that a persons soul and spirit are dual forms of the conscience. The soul is the base of emotions. We have a soul and a spirit because we have a brain. Without a brain we would have neither a soul, spirit or conscious. So a baby’s soul stems or comes from their brain.