In 1980 he was named pastor at Lynn's venerable, St. Mary Parish. Missionary zeal still burned in him and in 1987, Cardinal Bernard Law granted him permission to go to a whole new mission field as a lend lease priest to the diocese of Fort Portal in Uganda where he served for more than four years.

Returning to the US he served briefly as a parochial vicar at Our Lady of Lourdes in Brockton and then was granted a sabbatical which he took at St. Patrick Seminary, Menlo Park, Calif.

He returned to the archdiocese in early 1992 and was named at first parochial vicar and then pastor at St. Cecilia Parish in Ashland where he would remain for the single longest assignment of his priestly ministry (1992-2007). Just before leaving the parish, he celebrated the golden jubilee of his priestly ordination.

Granted senior priest status in 2007, he assisted in parishes until he moved to St. Patrick Manor, Framingham, then to Regina Cleri, Boston and most recently to Marian Manor in South Boston.

Merrimack Regional Bishop Robert Hennessey, himself a onetime member of the St. James Society, was the principal celebrant of Father Mulligan's Funeral at St. Cecilia Church, Ashland on Aug. 29 joining the bishop as concelebrants were Fathers David Costello, present director of the St. James Society; Dennis Dever, George Emerson and Ernest Pearsall, all former directors; classmates Msgr. Peter Martocchio, and Fathers Joe Gaudet, John Mulvehill and John Lizio; St. Cecilia's present pastor, Father Richard P. Cornell; Fathers Richard Erikson; Pat Universal; Paul Clifford; and Joseph Kane; Father John Sheridan was the homilist.

Father Mulligan's sole surviving sibling, Edwin died just 12 hours after Father Mulligan. So the funeral Mass at Ashland was celebrated for both brothers.

Following their funeral Mass, both Father Mulligan and his brother Edwin were buried in Oak Grove Cemetery, Medford.