The most likely reason a Civil War soldier didn't return home is that he died of disease or illness.
The fighting that occurred during the bloody Civil War resulted in thousands upon thousands of casualties. But while many lives were lost in battle, even more were lost due to disease. For every three soldiers killed in battle, five more died from disease. Dysentery alone accounted for almost 100,000 deaths in the Confederate and Union armies. Typhoid, pneumonia, tuberculosis, measles and malaria were also responsible for many deaths.