After graduating from the college, Morgan immediately enlisted in the 7th Indiana Infantry Regiment for around three months before his tenure expired and temporarily became a teacher at Atlanta, Illinois.

He went on to participate at the Atlanta campaign as well as the Battle of Nashville while being in the general staff of Oliver Otis Howard.

[2] In 1889 newly elected President Benjamin Harrison appointed Morgan the Commissioner of Indian Affairs in 1889 in order to promote education for Native Americans.

[3] Morgan viewed education as a quick path to for Native Americans to learn how to fit into the mainstream society.

To become civilized according to American standards an Indian youth had to learn new habits of dress, belief, and behavior.