Three years ago, Glasgow Museums director Mark O’Neill took a party of journalists around Kelvingrove Art Gallery and Museum when it closed for refurbishment. With a flourish of his arms he indicated how these offices to the north would be swept away, those windows would be opened up and the light would flood in, restoring one of the UK’s most visited museums to its former Victorian glory.

Today, his vision has been realised - and more.

Daylight streams into the central court where a century ago elegant marble statues and palm trees stood. The heavy stone pillars and balconies of the east and west courts have been stripped back to their original honey colour, and the Spitfire he envisaged hangs jauntily from the ceiling. Look up, look down or look around, and there is something out of the ordinary to catch your eye.

Some pound;27.9 million and a wealth of ideas has gone into the refurbishment of Scotland’s best loved museum. Design and intent are everywhere, from the rhinoceros threatened with extinction looking back at the dinosaur, to the wolf that could be reintroduced to our countryside facing towards the Scottish wildlife gallery.

The museum is divided in two: west of the central court are the Life (environment) exhibits, the east side has the Expression (art and design) displays. So, the west court houses Sir Roger the elephant (a favourite with generations of Glasgow children), a fresh-faced giraffe and cheetah behind him and the Spitfire and seagulls above. The east court is populated with Victorian characters, a hall of white marble busts leading to portrait paintings and a crowd of modern white faces suspended from the ceiling with laughs, smiles and quizzical looks.

Follow the Life trail and you move through Animal Superlatives - the fastest, the slowest, the tallest - to Mineral Beauty (rocks, crystals and jewellery) and Understanding Landscapes (paintings of the Clyde with Dumbarton Rock, created by volcanoes, and the Highlands, gouged by the ice age).

“The idea is that you look at the art, explore the content and perhaps get drawn into new interests,” explains the senior education and access curator, Sue Latimer.

Ancient Egypt has plenty to interest schools with three different stories: on men and boys, on the role of women and on life and death and the associated rituals. In the middle of the gallery lie a mummy and a sarcophogus and around the wall is written the story of life and death. A mix of interpretation, objects and interactive displays draws visitors into the story, inviting them to choose items for an offering.

Creatures of the Past is a gallery of dinosaurs and animals facing extinction. Tyrannosaurus rex is no more, wiped off the face of the museum by a ceratosaur, which towers over a large plinth with two glass cases containing, to the left, the long fossil of a dolphin-like ichthyosaur and, to the right, rocks from the late Jurassic era. Along the side is a timeline.

Move on past the threatened monkeys on a chair made of wood from the disappearing rainforests and you walk through one of the museum’s three discovery centres.

“You can stop here to study aspects of the environment in closer detail or, if it is closed off for a school party, move on to Scotland’s Wildlife,”

says Ms Latimer.

Scottish birds are displayed by season with recordings of their songs.

Under your feet is Wild About Glasgow, an aerial view of the city accompanied by an interactive display that homes in on sightings of animals and plants. A glass case contains the image of a tree trunk with associated insects, birds and butterflies pinned on.

Upstairs, a gallery on Cultural Survival tells the stories of different peoples across the world, from the Benin bronzes and the Masai herders to St Kilda and the last pearl fishers in Scotland.

Altogether 8,000 artefacts and artworks are now displayed in the Kelvingrove: that is 3,000 more than before. It reflects what the council describes as “a shift of philosophy from the Victorian approach to a 21st century view that is object based, visitor centred, interdisciplinary and intent on telling the most interesting stories about the objects on display”.

The key to the new arrangement is juxtaposition; for example, the case of soldiers’ armour arranged beside the animals whose defence systems inspired its design (the strong ridges of the clamshell are echoed in the reinforced helmet and the fingers of the metal gloves imitate the articulation of the crayfish).

When Mr O’Neill first revealed plans for mixing the museum collections with the art, there was a wariness among art lovers, who would not wish to see artworks sullied by dusty old animals and computer interactives. The artworks had always remained apart. On the whole, they need not have worried, for the surprise at Kelvingrove is how well the objects complement each other. The stories they tell are both fascinating and illuminating.

On the Expressions side, there are beautiful galleries of Dutch Old Masters, of French 19th century painting and of Scottish art. Following a successful trial at the MacLellan galleries, where the best of the collections were exhibited during Kelvingrove’s closure, these now have select quotations from the artists painted on the walls above. They also have interesting labels with up to 30 words in a typesize for all to see, and boardbooks visitors can pick up for further information.

The French gallery is vibrant with style and colour. It looks at changing styles from the 19th to 20th centuries, through pointillists to fauvists, with sections on portraits and still life, a look at composition and viewpoints. Paintings are paired to illustrate points, and a Picasso and Duffy are hung low especially for under-5s to study. A computer storybook follows Mr Duffy on a day that he goes out painting on the pier.

The Italian gallery includes not only Renaissance paintings and Venetian glassware but also 15th century armour and weaponry: this was an age of violence, Ms Latimer points out. A case at the centre looks at the craft of art, with dogs’ teeth to polish gold for gilding, colours from rocks, burnt wood for charcoal, stoats’ tails for brushes, goatskin for parchment and fish bones and eggs for glue.

Dutch Art includes a story on why art flourished in the Netherlands, how its wealth came from trade, the start of the middle class and people being able to afford paintings, and how artists created markets for, say, landscapes.

A Scottish Art gallery focuses on the Glasgow Boys and the Scottish Colourists. A portrait by James Guthrie is contrasted with a sentimental Victorian painting. The influences on Henry and Hornell (Japan and Celtic history) are studied, as is the French influence on the Colourists.

For the first time there is a special room dedicated to Charles Rennie Mackintosh and the Glasgow style, where elements of three Mackintosh tearooms sit alongside embroideries by the Macdonald sisters. There is an introduction to the Glasgow style, with sections on heart and peacock motifs, and a collection of chairs to illustrate the progression from early Victorian through Mackintosh.

Several galleries adopt a more radical approach. Scottish Identity in Art, for example, looks at how the view of Scotland is determined by history, authors and artists, notably the Jacobites, the battle of Bannockburn, Mary Queen of Scots and Robert Burns.

“The Victorian painting of Mary Queen of Scots shows her as beautiful and young when going to her death, but she was 44, grey haired and quite ill,”

says Ms Latimer.

A painting of Robert the Bruce shows him as Victorian hero, wearing chain mail and a crown, with a big sword in his hand. “The sword is anachronistic,” she says, “an example of one that would have been used 200 years later, so real medieval swords are on display.”

A section on landscape paintings, accompanied by geological specimens, is less successful, as too much clutter prevents you standing back to take in the scale and perspective of the artworks. And there is a sense in which hanging Raeburn’s portrait of The MacNab as a part of a display with bagpipes and a tartan dress denigrates the masterpiece.

However, these are bold initiatives, attempts at innovative and imaginative displays that nine times out of 10 work astonishingly well. And they are set up in a modular system that allows 10 per cent of the stories and displays to be changed each year.

There are so many new stories to explore, so many layers to unpick and lessons to learn - and all of it remains free. On July 3, 1,000 teachers are invited to explore the museum before it reopens to the public on July 11. They will be given a tour of the galleries, the discovery centres at the corners of each floor and the new education centre at lower ground level. They will be left with no doubt that the three-year closure and every penny raised for the refurbishment has been worthwhile.

The Kelvingrove New Century Project has been funded by Glasgow City Council, the Heritage Lottery Fund, the European Regional Development Fund, Historic Scotland and Scottish Natural Heritage. Members of the public also donated pound;5.5 million through the Kelvingrove Refurbishment Appeal.