With the beginning of the Second World War, thousands of people flocked to the Ypsilanti Area. The largest share of these people came to work in Henry Ford's Bomber Plant. During the first months a new community was born. This new community took the name, Willow Run. The late Cardinal Mooney, then Archbishop of Detroit, established St. Alexis during the spring of 1940 as a mission of St. John's Parish in Ypsilanti. Fr. Clare Murphy was the first priest sent to head the new mission. Father lived at St. John's Rectory and said Mass in the now demolished Willow Run Theater.

The first order of business was to locate facilities. The College purchased a number of buildings in Willow Run on Clark road and on Midway Street. These buildings included an elementary school building which had not been used for two years and was renamed. Also purchased was a condemned bowling alley which also had not been used in over a year. The Saint Alexis Church building was also purchased along with other associated buildings used by members and staff of Saint Alexis.