At first it went to a bomb shelter in the basement of a museum, then an art bunker built into the dunes on the North Sea in the Netherlands. Toward the end of the war it was hidden in a secured cave in Maastricht, a Dutch city near the Belgian border.

Starting in 1939, as war in Europe spread and the Nazi invasion of the Netherlands loomed, leaders of the Mauritshuis, the jewel box museum in The Hague, took extraordinary steps to protect Johannes Vermeer’s “Girl With a Pearl Earring” and other works central to its collection.

Wilhelm Martin, the museum’s director at the time, removed it and other famous works like Rembrandt’s “The Anatomy Lesson of Dr. Nicolaes Tulp” and Carel Fabritius’s “The Goldfinch” before the Germans arrived because he understood that they would be in peril, both from bombardments and from potential Nazi looting afterward.

The survival of these works, through strategic planning, diplomatic appeasement and the German affinity with the conquered Dutch as ethnic brethren, is now the subject of an exhibit at the Mauritshuis. “Facing the Storm: A Museum in Wartime,” which is on view until June 29, coincides with the 80th anniversary of the liberation of the Netherlands in 1945 and is based on extensive new research.

“It was a balancing act,” said Quentin Buvelot, curator of the exhibition. “Martin wanted to protect the people who worked there — a relatively skeleton staff — as well as the collection, and the museum building, and so he had to act in a certain way.”

The Mauritshuis took a “diplomatic” and “ambiguous” path to dealing with the pressures imposed by the Nazi occupiers, said Eelke Muller, a historian at the NIOD Institute for War, Holocaust and Genocide Studies in Amsterdam, which contributed to the research project.

At Rotterdam’s Museum Boijmans Van Beuningen, the director, Dirk Hannema, helped the Nazis loot work from Jewish collectors. Willem Sandberg, the wartime director of the Stedelijk, Amsterdam’s museum of contemporary art and design, on the other hand, helped hide art in bunkers for Jewish families and engaged in other forms of resistance.

The Mauritshuis found a middle ground, said Buvelot, in part because it was under the thumb of the Nazi occupation officials in The Hague, who held the purse strings to the museum. It was also physically adjacent to the Binnenhof, the parliamentary seat of power, which was teeming with German soldiers.

When Germany invaded the Netherlands in May 1940, the Dutch royal family and top state officials fled to Britain, leaving the country’s civil administration to fend for itself. Hitler appointed Arthur Seyss-Inquart, an Austrian Nazi, to run the occupied Dutch territories.

As part of their attempted conquest of Europe, the Nazis looted millions of paintings, sculptures, books and furnishings. Hitler and his second in command, Hermann Goering, were particularly passionate about collecting 17th-century Dutch art, especially Rembrandts and Vermeers.

Through outright looting or forced sales, agents acting for the Nazis made off with tens of thousands of artworks from private Dutch-Jewish collectors and dealers, including the Gutmann Collection in Heemstede and the Jacques Goudstikker Gallery in Amsterdam.

It would seem that the Mauritshuis’s trove of Dutch masters would have been a prime target for Nazi theft as well, but the nation’s public art collections were largely spared, said the cultural historian Frank van Vree, emeritus professor at the University of Amsterdam.

In France, after Hitler’s looters robbed French Jews, the Nazis also demanded art from the French national collections. However, Buvelot noted, the Germans never targeted the Dutch national collections in the same manner. That had a lot to do with the Nazis’ belief that their Dutch neighbors were “brudervolk,” part of a Germanic brotherhood, or were “genetically” kindred spirits who would adopt Nazi worldviews.

“Everything they saw as national property was actually really safe,” van Vree said. The Mauritshuis was required to lend art to Nazi headquarters and offices, Buvelot said, but it never had to relinquish art to Germany.

Van Vree said Germany’s cultural theory about the Dutch was “that they were considered to be equals.”

“And they considered the art of the Low Countries, particularly the 17th-century art, as part of the ‘lower German cultural area,’ which goes back to archaeology and prehistoric times, and this idea of a kind of historical continuity of the Germanic race,” he added.

Rather than loot Dutch museums, Hitler’s agents in The Hague used the institutions to try to indoctrinate this “fraternal” public into Nazi ideology, Muller said. “Culture was a very important element for both their propaganda and for their self-image,” she said.

In service of this idea, the Rijksmuseum, the national museum in Amsterdam, staged about 35 propaganda exhibitions throughout the war, van Vree said. In contrast, the director of the municipal art museum in The Hague, Gerard Knuttel, refused to use that institution for propaganda purposes, and was fired and sent to an internment camp for two years.

The Mauritshuis hosted five shows of Nazi propaganda, including displays of “German Books Today,” and amber objects, like gems and jewelry, because Hitler hoped to promote the Baltic Coast’s natural resource as “gold from the sea.”

Martin wrote letters of protest but allowed these exhibitions, Buvelot said, because he feared that if the museum was empty during the war, the occupation government would seize the building for its use.

Researchers also uncovered evidence that Martin may have allowed Dutch resisters to hide in the building, probably in the attic, Muller said. Martin wrote in a postwar statement that dozens of loaves of bread were delivered to the building each day, she added.

To protect the art collection, he created a color-coded priority system, and marked works with triangles in the colors of the Dutch flag: red triangles for national treasures; white for works of slightly less significance; and blue for art that could be replaced. Art with blue triangles remained hanging in the museum, alongside a lot of empty frames.

Vermeer’s “Girl With a Pearl Earring,” was marked with a red triangle. Unlike most of the Mauritshuis’s other artworks, the “Girl” remained in its ornate frame because of its priority status, said Abbie Vandivere, a paintings conservator at the Mauritshuis, who led a research project on the painting.

After the liberation of the Netherlands in May 1945, Vermeer’s painting was removed from the Maastricht cave where it had spent three years (its final storage spot after departing The Hague in 1939). “There’s no evidence to suggest that the ‘Girl’ got damaged either during the war or after,” Vandivere said. “I think that’s quite remarkable.”

The painting was then transported by truck to the Rijksmuseum for the exhibition “Reunion With the Masters,” which opened on July 15, 1945, and drew some 167,000 visitors during its run. The display of more than 150 artworks that had been safely retrieved from various depots reassured the Dutch public that the national heritage was safe.

“Girl With a Pearl Earring” was at last returned to the walls of the Mauritshuis in September 1945, four months after the end of World War II, and by November it was joined by the museum’s other artworks.

“In the end, there were few losses, and the museum was still there,” Buvelot said. “It all ended well for the Mauritshuis.”