On Tuesday morning at nine, teachers, administrators and clergy of the Pope John Paul II Academy gathered at St. Mark's Church on Dorchester Avenue to celebrate a new school year, and what they term a new beginning for Catholic education in urban centers across the United States.

"Into this project, over the last months, we have poured thousands and thousands and thousands of hours of work, countless Rosaries, meeting after endless meeting, and, through the extraordinary and, I would even dare to say, unprecedented generosity of our benefactors, many tens of millions of dollars," said Rev. Paul Soper in his homily at the Mass.

From there, the educators moved on to their respective five campuses across Dorchester to find new books, computers, science laboratories and many other wonders that money can buy. All saw their new schools save those who will teach at Neponset Campus which wasn't quite ready yet - though crews are swarming over it and Suffolk Construction executives will line up and swear it will be finished in time for the first day of school on Monday.

On Columbia Road, St. Margaret's blackened floors were sanded down and shine again, say those who have been inside, and some of the stained glass was painstakingly preserved. One former student commented that the path leading to the principal's office is just as she remembers it.

Trucks could still be seen unloading at St. Ann's on Tuesday, carrying new books and new computers, the finishing touches arriving just in time.

It's been a long hard road since the Reporter first broke the news of plans to close Dorchester's eight parish schools and create four regional schools in their place back in February 2007.

"We obviously need to do a better job on communication on our end," admitted Archdiocese spokesman Terrence Donilon at the time.

The greater level of transparency that followed, largely through meetings the following June and a series of options offered to parents at meetings that October created a plan announced just after Thanksgiving in November: to close two parish schools and create a system of five regional schools. By that time, St. Brendan's School had already opted out of the plan entirely.

"This will not be a top-down process, but it is being developed at the school level, with direct input from parents and principals," Donilon was able to say before it was all over.

Then came tears, speeches and celebration during the closings of St. Peter's and St. Kevin's schools. And over the summer the hiring process for teachers new and old, including some veteran educators who were not asked to come back and others who felt they were promised more pay in the new system.

Neither time came without tears and scattered feelings of betrayal.

But on Monday, as Soper predicted in his homily, a pre-K child will peer inside a classroom door, a third-grader will try not to look back and see if grandma is waving, and a gangly teenager will crack a smile at an old friend. The end very well may justify the means.

Even neighbors who have endured construction crews working double shifts and have taken issue with details will admit that it's good to see St. Margaret's as a school again - a.k.a. the Columbia Campus, as a few at Suffolk and the Archdiocese call it.

Some $69 million has now been raised, estimated Donilon, largely by former advertising exec Jack Connors, Suffolk Construction's John Fish, and former Fidelity fund manager Peter Lynch. Enrollment has reached 1,530, above the Archdioceses stated goal of 1,500 and very close to the number the seven schools previously taught in 2006.

Activity will fill the schools from 6:30 a.m. until 6 p.m., including music, arts and theatre programs at each say administrators, including a new collaboration with Boston College's Urban Ecology Institute that will teach kids about ecosystems in the city and how things like green building and open space affect them, perhaps creating the hard-nosed civic activists of the future.

"Dorchester and Mattapan need strong schools," said PJPII regional director Mary Russo, known locally as the former principal of Boston Public Schools' Murphy School. "The Murphy is a strong school, the O'Hearn is a strong school, and now the Pope John Paul will be a strong school. We need these strong schools because they are an anchor for the city. They keep people in the city."

Emmanuel College donated training for PJPII teachers and will mentor the new principals, Boston College is helping counsel students through a grant, and the new system which includes a board of directors dominated by laymen has created a spirit of collaboration that has yielded a holistic result, said Russo.

"That is one of the hallmarks of Pope John Paul, is to be able to offer [students] a very rich opportunity to develop in many areas," she said. "The regional model has been one of the most powerful forces in bringing about these changes. There is a powerful outpouring of talent."

Busing may become an issue, although administrators aren't showing concern yet. As of Wednesday Boston Public Schools, which recently put tighter restrictions on the bussing it provides for the city's public and private school students, told Russo the school would receive just one bus per campus and would be unlikely to receive any more transportation from the city in the foreseeable future due to budgetary concerns.

"We absolutely will be ready by Monday," assured superintendent Dr. Mary Grassa O'Neill.