James Watt is looking a little like voodoo's Baron Samedi this afternoon.

The Scottish inventor and engineer’s cold, hard face is divided neatly down the middle. The left half, as I look, is a dirty, stained brown. The right is pure, pristine, marble white. It’s as if Watt has been transformed into a caucasian Houngan (or priest if your voodoo vocabulary isn’t up to scratch). Appropriately enough it’s steam that’s been used to clean up the statue as it sits in the huge vaulted space of the Grand Gallery in the newly redeveloped (and now united) National Museum of Scotland.

In the city of Robert Louis Stevenson there’s something appropriate about this divided self. And maybe if we push the visual metaphor we can see Watt’s two-toned face as a symbol of the National Museum itself.

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Here, after all, is a complex that has sutured Benson and Forsyth’s beautifully monumental (and monumentally beautiful) 1998 sandstone mix-up of castles and Corbusier onto the Victorian gilded prettiness of the Royal Museum to create one huge complex with two distinct faces.

Of course, one of those faces has been little seen of late. The Royal Museum was closed in 2008 to allow a £46.4 million redevelopment scheme in a bid to refresh and revitalise an ailing old friend. “When I arrived in 2002 I suppose this building had a forgotten air about it,” admits Dr Gordon Rintoul, the director of National Museums Scotland. “Because the focus for several decades had been creating the new Museum of Scotland.”

As a result, he says, the building was something of a mess. “It had been mucked about with over the years. So I think what we realised very early on was we had a once-and-for-all opportunity to make a difference to the building and rescue it from all these ad hoc changes of a century and a half.”

After several hectic years the public will get the chance to judge the rescue bid later this week. Today, I’m fortunate enough to get an advance preview in the presence of Rintoul and Chris Coleman-Smith, director of Gareth Hoskins Architects, the practice behind the redevelopment.

There is still scaffolding up when I go in, some exhibits are uncovered, others swathed in plastic and wood, but these are minor marks on the bigger picture. The question is how does the building’s new face look?

The first thing you notice is in many ways the biggest change. Whereas before you entered the museum by climbing the steps in Chambers Street straight into the Grand Gallery, now you enter at street level through copper clad doors into a long arched basement that until recently has provided storage space. “We moved a million items out of here into storage,” explains Rintoul. Is that a figurative million or an actual million? “A million as in a million. Basically this was packed end to end as far as you can see.”

To refit for purpose, Coleman-Smith explains, they had to dig down over a metre, take out walls and open the space out, while at the same time bringing all the ancillary functions of the building down to the street level to free up exhibition space upstairs. They also had to cut out a big section out of the vault to allow for stairs and lifts. This basement – all bare stone and fair faced concrete – is where all the hard grind in the building was done.

If I’m honest it’s my least favourite part of the refreshed museum. Not because there’s anything intrinsically wrong with it, more for what it takes the place of. Because something has been lost in the process. Before, climbing the steps into that wonderful airy bird cage of a building always lifted the soul. The transition between the dark street and bright interior was thrilling. The suddenness of that immersion has been lost in the new entrance. Climbing the stairs from the arrival hall the transition is more gradual, less explosive.

Credit where it’s due though. Once you climb the stairs things improve substantially. The Grand Gallery is looking grander than ever. The goldfish that used to swim around in the pools have long since gone but so has much else – for the better. There has been a large-scale architectural decluttering.

“The building has become an exhibit,” suggests Rintoul. “Previously people seemed to regard the building as a problem. They walled all this in,” he says, indicating the arches on the first floor, “as if the arches were a problem rather than somewhere you look through and you see something at the far end which maybe draws your attention.”

It helps that the special exhibitions space that used to squat at ground level has been moved out and up. “It kind of sterilised the back of the building,” admits Coleman-Smith. “It opens everything up and encourages people up to the rest of the museum as well.”

In the past only 5% of visitors actually moved above the ground floor. “So a lot of what we were doing architecturally was encouraging movement and access and bringing back the clarity of the original Victorian building,” explains Coleman-Smith.

This is perhaps best seen near the south entrance of the building at ground floor level, where a 1920s staircase has been removed and you now look up to see the building’s bone structure. Angles meet and merge floor upon floor upon floor. By the time it opens, a bulldog twin trainer will be suspended from the ceiling in this elevation, its wings cutting through space. It’s one of 325 built in Scotland at Prestwick and it was flown by the Duke of Hamilton. Upstairs in the world galleries Maori war boats float over open space, a totem pole stands two storeys high. Led by the museum’s designers Ralph Appelbaum Associates, empty space is now seen as an opportunity.

And there’s so much space to use; 16 new galleries and 50% more public areas. In conjunction with this the exhibits have been substantially overhauled. “Once we started looking into it, it was clear we weren’t showing all the best stuff,” explains Rintoul. “No one had ever really stood back and said ‘what is all this stuff? Why have we got it? How does it hang together? So alongside all the detailed plans for the building we’re reassessing the collection. One benefit of moving everything out from the basement was that for the first time curators were almost forced to open boxes, see what they had and reassess everything.”

As a result 80% of the exhibits have not been on display before. There’s a feast bowl brought from Tahiti by a Scots merchant from Fife who went to the Pacific to make his fortune in the 1850s. He returned 40 years later with his Tahitian Princess wife and the bowl. “In many ways the starting point for a lot of the collections is Scotland’s engagement with the rest of the world.”

That’s the key here. Back in the grand gallery a massive menu wall, which starts at street level, climbs up the interior of the building full of stones, fish, bicycles; a smorgasbord of what you can find in the rest of the building. In this corner of Scotland you can find the rest of the world, it says. It’s a statement of the building’s intention and self-belief.

There is more work to be done. There are upper level galleries that still need to be reworked, more money to be raised to allow that to happen. But on first sight the facelift has worked.