The school was productive and successful, and the campus doubled in size to 880 acres with the purchase of the adjacent Parmalee farm. The new land was intended to be used for a Catholic university in the future. However, disaster struck on October 15, 1899, devastating the largest institution of the Chicago Archdiocese. A fire of undetermined origin, thought to have started by a dropped coal or candle, ignited the wooden chapel, and flames quickly spread to the administration building, barns, grain sheds, and shop buildings. The tiny Des Plaines fire department responded, but without working hydrants, could only wait for the fire to burn out; at the end, only the Villa remained along with a damaged Administration building and a couple small buildings. The 350 boys (as well as all the farm animals) living at St. Mary's were safe, but most had to be moved to other institutions until the school could be rebuilt; this effort was delayed greatly by Feehan's death in July 1902.
His successor, Archbishop James Quigley, decided to rebuild St. Mary's Training School on a far larger scale, consolidating in the two St. Joseph orphanages for boys and girls as well as the Chicago Industrial School into the institution. The Christian Brothers, who had previously operated the school, would be replaced by the larger order of the Sisters of Mercy. Plans prepared by Alfred Pashley were discarded, and by 1906, the rebuilt and re-imagined school, this time designed by architect William Brinkman, housed nearly 700 boys, as the north wing was completed. The new dormitory-style buildings included classrooms, indoor recreation, and a central kitchen with separate dining rooms by dormitory cluster. Each floor contained two dormitories, large rooms filled with beds, seperated by a common washroom. The consolidation, and rebuilt campus, was completed in 1911, and upwards of 1200 children could be housed at any given time. By the 1930s, the Sisters of Mercy had been replaced by the Sisters of Charity of Providence under Catholic Charities, and focus began to shift toward family-style living, allowing the children to develop individual identities; the halls full of beds were split into smaller halls with living rooms and their own restrooms, and siblings were kept together instead of divided by age.