During the early 1840’s, using a pen name, he carried on a newspaper debate on the topic of papal infallibility, in which he championed the Protestant position, with an anonymous Catholic writer. Scammon later admitted that the Catholic articles “hastened his conversion.” In 1845, Lieutenant Scammon was received into the Catholic Church at St. Peter’s Church on Barclay Street in Manhattan by Bishop John Hughes of New York. When Scammon admitted to Bishop Hughes that he had authored the Protestant articles, Hughes told him that he had authored the Catholic ones.
While stationed in Massachusetts, Scammon helped in the construction of St. Benedict’s Church in Springfield. After serving in the Mexican War, he resigned his commission and took up a teaching position at Mount Saint Mary’s Seminary in Ohio. At the outbreak of the Civil War he was President of Polytechnic College in Cincinnati. He volunteered his services to the Union and was named Colonel of the 23rd Ohio Infantry, where two future presidents (Rutherford B. Hayes and William McKinley) served under him. Scammon rose to the rank of Brigadier General and commanded a division, serving in the Eastern Theater of the war.
After the war General Scammon taught mathematics at Seton Hall College (now university) in New Jersey. He died of cancer in 1894, and the Archbishop of New York celebrated his funeral Mass at St. Catherine of Genoa parish in upper Manhattan. He was buried in Calvary Cemetery in Queens. General Scammon was remembered as “a man of winning manners; to his equals just and kind, but not familiar, and to his inferiors a rigid disciplinarian. In religion he was a sincere and devoted Roman Catholic.”