Roman in the Gloamin': with frantic preparations for the Pope's arrival in Scotland nearing conclusion, we explore the 'theologistics'

• Monsignor Michael Regan with the bones of St Andrew

Monsignor Regan will be carrying the bones of St Andrew.

These two holy relics, a shoulder blade and an unidentified bone fragment, each preserved in a glass reliquary, have not left St Mary's Cathedral since they arrived in Edinburgh from Italy in, respectively, 1879 and 1969. Monsignor Regan will place them before the altar of the chapel next to the Cardinal's home. There, at approximately 1pm on 16 September, the Cardinal and Pope Benedict XVI will kneel and pray for Scotland. It will be a quiet interlude during the nine and a half eventful hours the Pope is in this country.

What will be said during the prayer, who will be present in the chapel, how and when the relics are to be transported – each represents one of the tens of thousands of decisions taken on the run-up to the first journey of a Pope to Scotland since 1982. Those inside the process describe it as all-consuming. The visit by John Paul II had an 18-month run-in period. This time, organisers have had just five months to prepare.

Though the arrival of the Pope is considered a joyous event, there will be joy, too, on Thursday night when he is safely on a flight to London. As one church official puts it: "Everyone is holding their breath for an enormous collective sigh of relief."

Statistics alone give a sense of the level of management required. Seven hundred buses bringing 55,000 pilgrims from 160 towns to the Mass in Bellahouston Park. Police on every motorway bridge between Edinburgh and Glasgow. An expected 100,000 spectators in Edinburgh to watch the Holy Father go by.

The St Ninian's Day parade in Edinburgh is likely to supply one of the iconic images of the Papal visit, as the Popemobile passes along Princes Street with the Castle in the background. The crowd will be provided with 40,000 Saltires, and the Pope is to be preceded by a historical pageant, hundreds of children from schools named after St Ninian, and 1,000 pipers playing Highland Cathedral. This grand spectacle has been months in development.

Yet there is another dimension to this visit, a spiritual dimension, which takes the planning beyond what would be required for any other visiting head of state. The arrival of a Pope demands a whole new organisational discipline; we might call it theologistics.

Chief among the theologicians is Father Andrew McKenzie, the 45-year-old director of liturgy. It is his job to make sure that the Mass runs as it should. "Communion for a crowd of this size is a significant undertaking," he says. "One big challenge is working out a strategy for how to get communion to all of those people in no more than 30 minutes." It will take 400 priests to hand out the communion wafers. No wine, however. The Bellahouston Mass is alcohol-free. Nullus bevvius.

With less than a fortnight to go before the Mass, work has only just begun on the construction of the site. Bellahouston Park remains the calm province of sun-worshippers. On the day, however, a congregation of 70-80,000 will descend from as afar afield as Lerwick. The shortest journey, meanwhile, will be made by 1,200 church-goers from Our Lady of Lourdes in Cardonald. They plan to walk the half-mile to the park.

Among their number will be Rosaleen Beattie, who lives beside Bellahouston Park. She attended the 1982 Mass with her husband and children, and this time is taking three grandchildren and a deckchair. Back then, she flew the gold-and-white Papal flag in front of her house, having written upon it, in Gaelic, "100,000 welcomes to the Pope." She thinks that John Paul II may have seen it as he landed in his helicopter, and she plans to fly it in front of her home once again. "The atmosphere will be absolutely electric," she says. "I know it will."

In parishes across Scotland, people are busy preparing for the Papal visit. A key task is learning the music of the Mass. Rehearsals of choristers have been taking place since Easter. There will be an 800-strong choir in Bellahouston made up of singers from every diocese.

In Motherwell Cathedral, on a warm evening, one such rehearsal is taking place. The man in charge is John Pitcathley, who – as a young man – played the organ during the 1982 Mass in Glasgow and now, aged 53, has the honour of playing for the Pope once more.

There are around 70 people in the cathedral, mostly middle-aged and elderly. A few are on crutches. Getting around is clearly difficult. Yet they are here. Many kneel briefly before the altar and then take a seat on the pews, nattering with their neighbours. Before long, hosannas and alleluiahs rise to the roof beams. "Lamb of God," they sing, "you take away the sins of the world." As the sky darkens, the stained glass blackens till only the stars round the Virgin's head are visible. A woman sighs over a difficult part of the liturgy. "Aw that Latin," she says. "Oh dear."

The music, especially the Agnus Dei composed by James MacMillan, is incredibly powerful and everyone feels it. Afterwards, a few people stop and chat. One man in his late seventies recalls that in 1982 he, his wife and five sons went up to the altar and received communion from the Pope himself – "and to this day I cannot remember coming back down the stairs".

Anne McDermott, a chorister in her seventies, has tears in her eyes while explaining why she has made the effort to be here this evening. "For the love of the music and the love of the Church."

How important is the Pope's visit to her? "I couldnae describe it to you. It means my life to me. I'm 75 now, and it will never happen again in my lifetime."

It almost didn't happen at all. Last September, when it was first confirmed that the Pope would visit Britain, senior church figures were saying privately that they expected the visit would be confined to London. This did not please Cardinal Keith O'Brien. "It angered me intensely that the announcement just said England," he recalls. In October, the Cardinal went to the Vatican and put the case for Scotland.

Surprisingly, the planning process for the visit is not being run from any one command centre. There is no Papal hub. Instead, responsibility is shared by a range of priests and laypeople across Scotland. However, if one location could be considered key, it's an unassuming stone villa in Airdrie, just up the road from the Scooby Snax takeaway. The contrast with the marbled halls of the Vatican could not be greater, but here Father Paul Conroy, overall co-ordinator of the Papal visit to Scotland, has been on call 24/7 since March.

He is in frequent contact with the Foreign Office and Holy See, receives hundreds of emails each day and yearns for the slower era of epistles. Does he pray to God for strength? "I'm praying for good weather," he laughs. "And all the nuns in the convents, I've asked them to pray for good weather as well."

Those prayers are being answered a little too early, perhaps. On Friday evening in Glasgow it is certainly sultry, the pubs packed for the Scotland game. But in the Catholic Chaplaincy of Glasgow University, near the thronging Byres Road, there is a different kind of thrilled anticipation. Here, they are holding an all-night prayer vigil for the success of the Papal visit.

The large crucifix above the altar is draped in gold and white silk. There are a couple of dozen people in the chapel by 9pm, most of them students in their twenties. These are regular young people with BlackBerries, hoodies and Facebook pages, albeit pages which carry banners pledging support to the Pope. The air smells of incense, and there is that intense atmosphere of concentration and joy you sometimes get with silent prayer.

Last week, The Catholic Herald asked whether indifference was the greatest threat to the Papal visit, and a poll showed that 63% of Scots, most of whom considered themselves Christians, were neither for nor against Benedict's arrival in Scotland. Against this backdrop of apathy, it's hard not to be impressed by the passion and commitment of those singing at the Motherwell choir rehearsals, or those priests grafting to make the Papal visit happen, or Rosaleen Beattie with her flag, or the students praying all night by candlelight that everything comes good.

Louise Rocks, a 24-year-old studying for a chemistry PhD, sums it all up with a profoundly Scottish slant on the visit of Benedict XVI. "I'm so excited that the Pope is coming to Glasgow," she says, taking a break from prayer. "It's going to be like T in the Park, but better."