In a dispiriting age, ruled by market forces, a museum's value to humanity can easily be overlooked. But what actually is the point of museums today? On hearing that pesky question, Gordon Rintoul doesn't wince. Over the course of more than 20 years he has often encountered its upstart impertinence, and it hasn't yet defeated his grand goals.

"Museums are part of the cultural nexus that makes life enjoyable and worth living," he says. "They also tell us quite a bit about ourselves: how our world has come to be the way it is; our place in it, and what that might mean for the future."

But next month Rintoul, director of National Museums Scotland, will set about demonstrating the importance of museums in our lives by paradoxically packing up and closing down a much-loved chunk of the Royal Museum in Edinburgh for the next three years.

The reason? A radical transformation with a price tag of £46m which will bring the 21st century into the landmark building while honouring its past. Even so, to the outsider this might seem reckless. More than two million irreplacable artefacts will need to be wrapped, labelled and crated to storage in Granton.

Does Rintoul lie awake, ambushed by dread of what might go wrong? "No. Everyone involved has put such a huge effort into thinking through all aspects of the project. And throughout my career I've somehow ended up in roles where I've been responsible for doing new things. None of this scares me: I've been here before."

Those three words, "doing new things", rather underplay Rintoul's expertise. This is the man who, three years ago, made an audacious pitch for Concorde, and won, then oversaw the dismantled silver bird's remarkable odyssey from Heathrow to the National Museum of Flight at East Fortune in East Lothian.

"Actually, that Concorde adventure has been the high point of my career so far. I just thought it would be a wonderful iconic acquisition for Scotland, but I knew it would mean massive challenges."

Rintoul was in a meeting when the call came through from British Airways, telling him he could have one of the decommissioned aircraft provided he undertook its transport to Scotland. Problem was, it couldn't be flown to East Fortune because the airstrip there was inadequate for a Concorde landing.

"Straight away I said fine' and the team thought I was mad. I had no idea how we would manage to get the plane up here - but I didn't tell them that because they thought I had a grand plan."

In the event Rintoul's colleagues, plus police, Royal Engineers and Special Branch, rose to the occasion. The wings and tail fin travelled by road, and the fuselage by barge up the Thames, then onwards by North Sea. In all, the voyage took more than a month. But why was Special Branch involved? "They had to check us out because we wanted to make a historic stop on the barge outside the Houses of Parliament."

Now, in temporarily closing more than half a monumental museum which attracts 800,000 visitors a year, he dates his fearlessness from when he first joined the museums business in the 1980s. "A different, younger generation of directors was coming in; people like me who had loved museums as children, but whose aim now was to polish up their dusty image and bring them back to life. Today that's even more necessary. Anyone running a museum now has to be much more entrepreneurial than 20 years ago."

In 1984, Rintoul defied sceptics by launching the Colour Museum in Bradford, funded by the textile industry. The first venture of its kind, it attracted more than 25,000 visitors a year by 1987, and gained such accolades as Best Museum of Social and Industrial History in Britain.

A Glaswegian born in Scotstoun, and a physics graduate of Edinburgh University, Rintoul moved to Widnes in Cheshire that same year to open Catalyst, a chemical industry museum that again confounded doomsters. By the time he had left it in 1998, more than 60,000 paying visitors were traipsing around its experiments and working displays. Among several prizes, the Gulbenkian Museum Education Award is Catalyst's proudest.

Sheffield was Rintoul's next destination, in 1998. As chief executive of its Galleries and Museums Trust, his task was to revitalise the city's ailing cultural status by opening a £15m complex part-funded by the Millennium Commission and developed in partnership with the Victoria and Albert Museum. When he left there in 2002, visitor figures were at half a million. As before, his credo was practical and direct: museums had to operate with efficiency and vision. They had to become not just repositories of gifted treasure but places of life-long learning for the widest constituency. In 2002, on his return to Scotland as director of NMS, Rintoul took on responsibility for five museums, a collection of more than four million items, a revenue budget of more than £20m and 475 employees.

All of which leads us back to his present preoccupation. On April 27, the first phase in the transformation of the main hall and basement of the Royal Museum will begin. By the middle of 2011, the finished result, he promises, will be spectacular. New approaches to learning are key. "We want to enable visitors, young and old, from all backgrounds to feel excited and inspired by what they see."

He says he doesn't care much for the phrase "social inclusion". "It doesn't really mean anything to anyone other than administrators. But yes, I certainly believe museums should be for everyone, and maybe that's because I was brought up in Glasgow without a silver spoon in my mouth. Yet, like huge numbers of others, I was often taken to Kelvingrove: always an adventure, always a major treat.

"As a country we've got a massive challenge there, and that's one reason why, 18 months ago, we opened the Connect gallery posthumous home to Dolly the cloned sheep which is now by far the most popular gallery in the entire museum complex." Connect, and the Communicate gallery, will remain open to the public throughout the building works, along with the adjoining Museum of Scotland. Gareth Hoskins, the Glasgow architect, has been chosen to accomplish the transformation, which so far has received financial awards of £34m from the Heritage Lottery Fund and the Scottish Government. Fundraising is expected to bring in a further £12m.

Sixteen new galleries will display thousands of extra treasures which have hitherto languished unseen. Among them is the Nobel Prize gold medal awarded to Alexander Fleming for penicillin in 1945. A three-fold increase in facilities for learning will provide the latest interactive technology to within a mouse click of visitors.

Extended displays in the natural history zone will demonstrate the diversity and evolution of the animal kingdom. Taking centre stage, will be a custom-built Tyrannosaurus Rex skeleton, its plaster-cast bones taken from fossils found in the American west. Increased space will also be dedicated to world cultures.

But before the anticipated millions reach all this, they will arrive at a handsome new entrance on Chambers Street leading down to an entirely new floor, previously a storage catacomb. This will house the museum's main restaurant and shop. Glass lifts and gleaming escalators will transport people to the main exhibitions in the enhanced A-listed hall with its soaring roof of wood and glass, and cast-iron construction. The pulling power of the hall for visitors has always been unparalleled, and to mark this distinction it will be renamed the Grand Gallery - the only surviving example of an architectural style designed for the Great Exhibition at Crystal Palace in 1851.

If Rintoul could run away with just one piece of booty from the museum, what would it be? "Fleming's Nobel Prize medal, because the discovery of penicillin has had a huge impact on lives across the world. I was astonished to find that the medal was just one of the fabulous world-class things we possess but don't have on display. So, now, when the transformation is complete, we'll be able to rectify that."

Fleming's medal, for Rintoul, is one small treasure with vast, symbolic meaning - a priceless gift among many, he says, that will ignite curiosity, sparking a desire to learn more. Which is why museums matter. So, should the cry ever go up "Down with Museums", Gordon Rintoul will be ready for that other challenge: the barbarians at the gate.