What is interesting about this decision is how the Supreme Court was able to draw a fine line that allowed the rule of law to continue, yet not to such a point that it would interfere with Congress' post-war actions in the now occupied South. At the time of the decision, Congress was held by a Republican majority. What this case holds is that because the South seceded, during the war they and their courts did not uphold the authority of the Constitution. Thus, habeas corpus could be suspended and trials against military officers and civilians could occur in military courts....

Therefore, because of this decision, the punishment of occupied south could occur as planned.
This decision is in sharp contrast to decision handed down prior to and during the Civil War. During that time period the focus was on maintaining the unity of the entire country and therefore the decisions were equal and fair, looking to the south as still part of the United States. However, after the war finished, the Northern victors, through congress, implemented the contiguous program known as reconstruction, which held the Confederate States as being rebel states and thus not yet fully part of the Union. The Ex-Parte Milligan decision is essentially the Courts granting legality to reconstruction.