During this period, Saint John was second only to Grosse Isle, Quebec as the busiest port of entry to Canada for Irish immigrants.

The periodic outbreaks centered largely in the poorer Catholic district, where people were scarcely over the effects of ship fever (typhus).

Connolly also previously contacted the Sisters of Charity of St. Vincent de Paul in New York to staff a planned orphanage.

It is uncertain whether she entered with the intention of returning to Saint John to work with Bishop Thomas Louis Connolly, who had begun a number of initiatives on behalf of poor immigrants, or whether she intended to remain in New York.

She and three companions returned from New York to New Brunswick and, on 21 October 1854, made their vows as Sisters of Charity of Saint John, a new diocesan religious congregation.

Archbishop Connolly attended the Vatican Council of 1869–70 and was among those opposed to the issuance of a Dogmatic Constitution regarding papal infallibility as he felt that the political climate was not right for the church to confirm the doctrine.

Archbishop Connolly in 1865 wrote:[6] There is no sensible or unprejudiced man in the community who does not see that vigorous and timely preparation is the only possible means of saving us from the horrors of war ... To be fully prepared is the only practical argument that can have a weight with a powerful enemy, and make him pause beforehand and count the cost.Connolly believed strongly that the Irish in Canada fared better than those in the United States.

Nicholas Flood Davin wrote: "He belonged to the great class of prelates who have been not merely Churchmen, but also sagacious, far-seeing politicians and large-hearted men, with admiration for all that is good, and a divine superiority to the littleness which thinks everybody else wrong.