Kelly was selected by the Christian Brothers Superiors to help in the establishment of a Second Novitiate at the General Motherhouse in Lebecq-les-Hal, Belgium.

[1] Kelly was the President of De La Salle College in Manila when the Japanese army invaded the Philippines on 8 December 1941.

In January 1942, Japanese troops forcibly entered De La Salle College and began to occupy all but a small portion of the building.

The Irish Brothers were left to the chapel and a few small rooms while the American De La Salle Christian Brothers were interned, first in a retreat house of the Society of Jesus at Santa Ana, Manila, and then in a Spanish hospital in San Pedro, Makati.

They were later put in a Japanese concentration camp in Los Baños, Laguna, until they were rescued and freed together with their other fellow clergy-prisoners by the American Forces under General Douglas MacArthur in February 1945.