He initially ministered to Confederate troops including the Montgomery Guards, an Irish company established in Savannah for the First Georgia Volunteer Regiment.
Whelan heard about an appeal for priests made by John England, the popular and dynamic bishop of the new Diocese of Charleston, which at the time comprised both Carolinas and Georgia.
For the next two years he served as secretary to the bishop before beginning his duties in communities throughout North Carolina, including New Bern, Washington, Greenville, Fayetteville, Lincolnton, Salisbury, Wilmington, Long Creek, and Raleigh.
Located on an old stagecoach road running from Sparta through Double Wells to Raytown and Washington, the original place of worship, constructed of hand-hewn logs, was also the first Catholic Church built in Georgia.
Two years later another report summed up Whelan's whole pastorate: "In the diocese…there is not a congregation, remote and rural as it is, in which, taking proportionate numbers into the scale, we find the youth are more moral, orderly and better instructed.
[6] The young diocese was without a bishop until the Reverend John Barry, the interim administrator, was consecrated in August 1857, and Whelan was appointed his vicar general.
As they readied the fort for action, Federal ordnance was being landed in the darkness and stealthily put into place behind sand dunes a mile away.
Sharing the everyday life of the men in all ways, save military duties, he now had to bring consolation to the hard-pressed, weary soldiers.
On St. Patrick's Day, 1862, after morning Mass, Major John Foley of the garrison formally presented the flag to Private Bernard O'Neill, the appointed standard bearer.
The new rifled cannons proved to be a most effective advantage for the Union Artillery, providing greater distance and accuracy than that of their Confederate counterpart.
The officers were quartered in barracks and granted freedom of the island on their word not to escape; they were also issued blankets and limited supplies and money from home.
He added that he had successfully applied for a position as chaplain at the prison and had been granted the opportunity to offer Mass each morning in Castle William.
Quinn, in the name of all the clergy of New York, requested that Whelan be released on parole and be allowed to live at St. Peter's due to his age and his misfortune in having been captured while temporarily visiting Fort Pulaski.
On May 10, Loomis sent Whelan to Assistant Provost Marshal Hunt, who brought him before General John A. Dix and Judge Edwards Pierrepont.
As the exchange drew near, some prisoners, including O'Neill, decided to take the oath of allegiance to the Union rather than return to Georgia.
While passing through the lines at Aiken's, one of the Confederates improvised a staff and triumphantly hoisted the unfurled flag amid the loud cheers of the whole company.
[13] Before returning to Georgia, the chaplain visited Mount Hope Hospital near Baltimore to thank the Sisters of Charity for their gifts to the imprisoned soldiers.
His coat is not of the latest nor approved fashion: the sleeves exposing some inches of the lower part of his arm, and a large rough hand.
Before departing, the sixty-two-year-old priest, along with Father Hamilton visited Major General Howell Cobb, a Georgian with close ties to the Confederate administration.
After a restless night on his bunk in a little twelve-by-eight foot hut about a mile from the prison, he rose each day at dawn, took a scant breakfast and said his prayers.
As thousands more prisoners came and milled about its banks, some of the very sick were unable to extricate themselves from the mire; others who could not reach the "sinks," as they were called, had to relieve themselves in the mud.
He became sick with continual vomiting and later wrote: "Whelan decided that I should leave, so I took the trains back to Savannah whilst the…old priest retraced his steps to the stockade."
With this, he went to the town of Americus, purchased ten thousand pounds of wheat flour, had it baked into bread and distributed at the prison hospital at Andersonville.
"[33] A sergeant, John Vaughter, in his memoirs remarked that, "of all the ministers in Georgia accessible to Andersonville, only one could hear this sentence, 'I was sick and in prison and you visited me,' and that one is a Catholic.
Immediately east of Savannah's Catholic cemetery on the Thunderbolt Road, the federal engineers began reconstruction of the old Confederate earthworks.
[35] Whelan was the first to protest with a letter to General Quincy Gillmore, whom he had known at Fort Pulaski: "It must be…an extreme military necessity when the ashes of the dead are disturbed….
Since General Winder, the commandant, was dead, the cry for expiation began to focus on Captain Wirz, who had been in charge of affairs within the stockade.
They testified under oath that, although Wirz used profane language and occasionally spoke harshly to some of the prisoners, they had not seen him inflict any personal harm that caused death, nor had they heard of such injury.
[37] It seems that Whelan regarded Wirz as merely a symbolic scapegoat, made to pay for all the suffering endured by the citizens and soldiers of the North during the war.
Before this outbreak he had written to Secretary of War, Edwin Stanton, asking for $400 to pay back his loan from Henry Horne to procure bread for the Federal prisoners.