On May 4, 1900, a parish meeting was secretly called and it was to honor Father Cassidy. The parishioners found out that Father was going to Europe. A committee called upon Father and presented him with a well-filled purse containing well over four-hundred dollars, and the following address: "Beloved Pastor: Having learned of your proposed trip to Europe, we take this opportunity of paying you our respects before your departure. Fourteen years you have been the parish priest of this congregation and during that time, you have endeared yourself to all who have come in contact with you; and to us you have been a spiritual advisor and faithful friend. You have been a devout and untiring laborer in the vineyard of the Lord, and while we all very much regret that we are to be separated from you for the next few months, we still are more than compensated by a knowledge of the fact that it will be to you a season of needed rest and recreation. It is our sincere wish that your entire trip will be one of pleasure and that you will return to us in the autumn with improved health and vigor for the work before you. We know how badly you need a vacation, and we sincerely trust you will be able to put aside all cares and fully enjoy your tour in Europe, and particularly the visit you have in view to the land of your birth. We hope to receive word from you from time to time, and you may rest assured that although we may not be present with you in body, our best wishes and thoughts will follow you in your sojourn abroad. As an evidence that your work has been appreciated and that the seed sown in your labor among us had not all been cast on sandy ground, and as a token of personal esteem, we present you a purse, the contents of which we trust will help defray the expense of your trip, the recollection of which, we hope, may be a pleasant memory during your absence. Signed in behalf of the congregation, O.F. Biglin, Chairman of the Committee." Father Cassidy had a loving place in the hearts of his people and this was deeply exemplified on Sunday when he bid adieu for a time and there were tear-stained faces in the congregation as he told them of his departure. On Monday, May 7, 1900 Father Cassidy left by train waving goodbye to a large crowd assembled at the depot to bid him a safe trip and God-speed. He visited Rome, Germany, France, and the famous passion play at Oberammergau. On his return, he spent a month in Ireland and returned on September the first. The building of the foundation of the school continued.

On May 31, 1900, the Frontier carried the following article: Work on St. Mary's convent is being pushed forward rapidly. John Hunt has the contract for the brick work and has seven bricklayers at work. He expects to have the brickwork completed by August 15.

On June 11, 1990, the plans for the new Saint Mary's were shown and it was to contain four schoolrooms on the first floor, four school rooms on the second floor, with a dormitory in the roof which would be sufficient to accommodate one hundred pupils with sleeping apartments. The basement had a ten-foot ceiling, eight feet above the ground; the ceiling of the first floor was twelve feet, and on the second floor, eleven feet. The intention was to have it completed by September 1, 1900, with the estimated cost of thirty-thousand dollars, and the front of the building being built of pressed brick. On June 16, 1900, the Feast of Our Lady of Perpetual Help, the corner stone to the new school was laid by Father Opava, the temporal pastor, in the absence of Father Cassidy. Work on the new building progressed rapidly, and on October 7, 1900, the Feast of the Most Holy Rosary, a statue of Our Lady of Perpetual Help (the official title of the new convent) - a gift of Doctor Corrigan of O'Neill, was solemnly unveiled and dedicated, and on the following day was erected in the niche above the main entrance to the convent. Not a single accident occurred during the entire time of work on the construction of the building. During the summer months though, several Sisters arrived as an increase to the community which then numbered ten. On September 10, 1900, following a High Mass in honor of the Holy Spirit, the first school year in Saint Patrick's Parish was begun. One-hundred-and-six pupils were enrolled the first day. With the permission of the Bishop, two classes occupied the church, the Blessed Sacrament having been placed in the sacristy. A third class took up its abode in the City Hall (skating rink), a favor of the city Mayor Edward F. Gallagher. As the small house in which the Sisters lived temporarily did not provide sufficient room for all, several Sisters slept in an unoccupied house near the new Convent. It had been offered generously for their use, gratis, by kind neighbors. By the end of October, one wing of the new building was sufficiently completed to permit the Sisters, in case of necessity, to dwell in it, although there were as yet no banisters on the stairways, no plastered walls, no finished floors, etc. On October 29, after spiritual exercises were ended, the statues and pictures belonging to the Sisters were carried to the convent and after seven o'clock that morning, generous and kind-hearted people appeared with horses and wagons and transported all the belongings of the Sisters from the cottage to the new Convent. The Sisters were delighted to be united again under their own roof.

The school continued toward its building completion. After a lapse of several weeks, the new classrooms were gradually finished and ready for occupancy. On December 12, 1900, on the Feast of Our Lady of Guadaloupe, the convent and school were solemnly dedicated by Father Cassidy. A solemn High Mass was celebrated and Father Cleary, a renowned speaker from Minnesota, delivered a most eloquent sermon on the occasion. He outlined the benefits of a Catholic education and reminded the people of O'Neill that they were deeply indebted to the Sisters for providing these benefits for them. The rather large chapel did not furnish sufficient room for all who attended the services. The O'Neill Public School gave a free day to permit teachers and pupils to attend the solemnities. Many people wept through joy and gratitude at seeing their desires finally fulfilled. The Sisters and the people had given up many of the things that make life easy to see the school completed. The Stations of the Cross in the Sisters Chapel and the "Ave Maria" (the bell in the tower) were gifts of Mrs. James Gallagher - Ella Dailey Gallagher. The following inscription was upon the bell: "Ave Maria, Auxilium Christianorum, Protect All the Inmates, Bless the Benefactors, Pray For O'Neill, Assist Us In Death." On Christmas Eve, 1900, the Angelus was rung for the first time from the convent tower and Mother Kostka, Sister Alcantara, Sister Crescentia, Sister Laurentia, Sister Catherine, Sister Mathildae, Sister Sophie, Sister Geralda, Sister Norberta, Sister Eberharda, Sister Antoinette and Sister Arsenia were the Franciscan Sisters of O'Neill.

In April, 1901, Bishop Richard Scannell came to O'Neill and administered the Sacrament of Confirmation to two hundred-and-thirteen children. He expressed his surprise at the splendid achievements in such a short time at O'Neill. He inspected the new convent and was moved by seeing the poverty of each Sister's cell. He promised to send a second priest to O'Neill so that daily Mass could be celebrated in the convent chapel. And as the first school year closed, there were two-hundred-and-ten day students and twenty boarders.

On June 18, 1903, the initiatory commencement of the Academy of Our Lady of Perpetual Help took place at the opera house in O'Neill. Seven young ladies (Margaret M. Barrett, Agnes F. Clark, Rose E. Grady, Margaret M. McGreevey, Florence E. Mullen, Anna S. O'Donnell, and Mary M. Hagerty) received the first diplomas from the Academy which was hailed as one of the finest educational institutions in the state and is a credit to this part of Nebraska and was the pride of O'Neill and Holt County. And the younger students of the school presented the entertainment which consisted of a "dumb-bell-drill" and a "flower circle" by the lower grades, a military drama "Rising of the Man" was also presented and appreciated by the large audience, many of whom had come many miles to be present at these exercises.

In November, 1904, the pupils of the school contributed a quilt to the fair. It was artistically made of silk materials with the signatures of the O'Neill citizens worked on each block. The quilt was raffled off and won by Miss Maggie Cullen and the ten dollar gold piece was won by D. A. Doyle. Events such as these were aiding in planning the new church. In 1907, Father Cassidy bought the Sisters a gasoline engine and machinery for mixing bread at the Academy. Mixing by hand all those large quantities of bread needed for the convent and school was a tedious process and the machinery would greatly reduce the amount of labor in this line.

1908 brought a new dimension to the school. It was approved for a Normal Training program which produces certified teachers at the end of two years. It was for Juniors and Seniors and the program was incorporated into the regular school curriculum. This year also saw the formation of a St. Mary's Alumni Association with 51 members.

A new addition was being added to St. Mary's Academy to make more room for the boarders. But it was a severe winter and thus progress was slow and a severe storm hit with high winds and blowing snow on May 1, 1911. Bishop Keane did make it to O'Neill from Cheyenne to confirm 227 persons even though there were outbreaks of measles and small pox. But the new addition was finally completed and dedicated.

Bishop Harty, who succeeded Bishop Scannell (died in January, 1916) as Bishop of Omaha, visited O'Neill on October 27, 1916, and confirmed eighty-eight children. The Bishop received a gift of six thousand dollars from the parish for the purpose of helping build the new cathedral in Omaha. Spanish Influenza (Black Flu) in 1918, coal strikes at the coal mines in 1919 and scarlet fever in 1920 caused much discomfort in O'Neill and its schools.