Duggan was appointed as coadjutor archbishop of St. Louis and titular bishop of Gabala by Pope Pius IX on January 9, 1857 to assist Kenrick.

[1] While coadjutor archbishop, Duggan also served as administrator of Chicago for a second time when Pius IX accepted O'Regan's resignation in June 1858 for health reasons.

[4] The German immigrants, the largest Catholic community in the diocese, resented that the pope had chosen O'Regan, an Irish cleric, as their bishop.

[2] After arriving back in Chicago, Duggan in 1868 closed the seminary on the Saint Mary of the Lake campus and converted it into an orphanage.

Duggan invited the Sisters of Charity to open St. Joseph's Hospital in Chicago that same year; he provided them with furniture and beds from the closed seminary.

[10] On April 14, 1869, Pius IX ruled that Duggan was no longer mentally capable of performing his duties and sent him to a sanatorium operated by the Sisters of Charity in St.

[11] Pius IX named Reverend Thomas Foley from the Archdiocese of Baltimore as coadjutor bishop to administer the diocese, filling that role until his death in 1879.

[12] In September 1880, Duggan was sufficiently rational to sign a letter of resignation as bishop of Chicago, allowing the pope to appoint a new one.

On March 29, 2001, the archdiocese moved Duggan's remains to the Bishop's Mausoleum at Mount Carmel Cemetery in Hillside, Illinois.

At the reinterment ceremony, Cardinal Francis George spoke about rectifying the injustice that had been done to Duggan and the stigma of mental illness [2]