When John William Waterhouse’s painting Hylas and the Nymphs was removed from the walls of the Manchester Art Gallery at the end of January, all hell broke loose. Social media was electric with outraged cries of “censorship”. The critic Jonathan Jones asked whether this was the thin end of the wedge: would Picasso be off the walls next?

An Oxford professor of German wrote to the Guardian warning that this had happened before: Nazi curators had taken down works because they had “conflicted with their political aims and puritanical taste”. Messages poured into the museum’s website: some in support but more of them against. There were worries that the removal was an act of politically correct virtue signalling; wasn’t so far down the line from book-burning; was feminist extremism “at its worst”. There was also plain old irritation that a much-loved painting was not on view when visitors had travelled to see it.

Sonia Boyce, the artist at the centre of the row, was completely taken by surprise by the ferocity of the response to the temporary removal, as was the museum. Perhaps naively, given the timing: the culture wars were raging, a fourth wave of feminism was surging, the revelations of the conduct of Harvey Weinstein and others were reverberating around north America and Europe, and there was, and is, an upsurge of anxiety about how to deal with art made under different ethical conditions from our own.

Hylas and the Nymphs by John William Waterhouse. Photograph: Courtesy Manchester City Galleries

Boyce’s first instinct, she tells me, was to “go and hide – and not because I felt remorseful”. There was, she says, “a level of anger and vitriol that was really unhealthy”, and “the desire to bash women in the public space was strongly felt”. She also felt that the response fell into a pattern of outrage directed at contemporary art that runs deep in British culture: she was reminded of the “Tate bricks” scandal – a furore that broke out in 1976 over Carl Andre’s minimalist sculpture, Equivalent VIII, consisting of an arrangement of fire bricks. “There is an assumption that contemporary art has got to be nonsense, got to be a fraud,” she says.

The removal of Hylas and the Nymphs was described as a “publicity stunt” in some quarters, but that is a misinterpretation, she insists. Taking the picture down had been about starting a discussion, not provoking a media storm. And, as she argued in a Guardian article, it was by no means censorship. It was certainly not about removing an image deemed to be offensive. Rather, it was drawing attention to – and questioning – the ways in which museums make decisions all the time about what visitors see, in what context, with what labelling. The way Boyce explains it, the action was not so much about removing Hylas and the Nymphs, making it invisible (although, of course, it did do that, if only for a week). Rather, it was about making the hidden workings of museums and their curators baldly visible, and inviting members of the public to take a view. Which, you might observe, they did. Though not, perhaps, in the way that Boyce or the gallery had expected or intended.

Boyce and I meet at her studio in east London, a converted shipping container tucked into a loop of the Thames at Trinity Buoy Wharf, a peaceful clearing among the city’s seemingly endless forest of new-build high-rises. She has just moved in; everything is in boxes. Just now, she is also rushing to finish editing her new work, Six Acts – a film intimately connected to the Hylas scandal, which will be the culminating point of her retrospective at the Manchester Art Gallery when it opens on Friday.

Boyce in London. Photograph: David Levene/The Guardian

In a way, with this studio, she has come home: born in 1962, she grew up nearby in Canning Town, and it was at school that an observant art teacher, Mrs Franklin, noticed Boyce’s almost obsessive habit of drawing – in the margins of exercise books, anywhere. The teacher encouraged Boyce, at 15, to start going to life-drawing classes. Boyce’s family was one of avid day-to-day creativity. Her mother, a nurse, was always dressmaking, and there was always music, and making of one kind or another, around her and her siblings as she grew up. But she hadn’t thought of “being an artist” as a possible career until her teachers encouraged her to try an art foundation course, where her feminism was sparked.

Afterwards, she attended college in Stourbridge in the West Midlands. “It was very clear when I was at art college that I was somehow out of place; the system hadn’t anticipated me, or anyone like me,” she says. “Even though there were a lot of female students, they were thought about as though they were being trained to become the wives of artists, not artists themselves. As a black person, there wasn’t a narrative at all. Maybe to be a model.”

She herself has always taught: the conversation, the to-and-fro about ideas has been necessary to her. “The art school,” she says, “is like a laboratory.” As a young artist in the 1980s she was part of the black British arts movement, and her early work was quite often about literally drawing herself into a national history from which people of colour had been excluded. When she was 25, in 1987, the Tate bought a drawing she had made a couple of years earlier called Missionary Position II. She was the first black female artist to enter the collection. In 2016, she became the first black woman to be elected a Royal Academician. It is a history of barrier-breaking that she puts down to sheer “stubbornness about keeping going”.

Liquorice Black at the Manchester Art Gallery takeover. Photograph: Sonia Boyce

To understand what was really going on with Hylas and the Nymphs, it is necessary to spool back in time. Boyce was last spring having meetings with curators about plans for her exhibition. One of them, Clare Gannaway, asked Boyce if she would also be willing to take part in the museum’s public events programme. The institution regularly runs what it calls “takeovers”, where an artist is invited to intervene in the permanent collection in some way. Boyce was fascinated by Manchester’s particularly rich 19th-century collections, not least an 1826 portrait by James Northcote of Ira Aldridge, the first black actor to play Othello in Britain.

She began to have conversations with staff about how the work in the galleries is selected, displayed and interpreted. Lots of colleagues wanted to join in – curators, cleaners, gallery attendants, volunteers. Quite a lot of those involved were women “uneasy about the way gender was represented in the galleries”, says Boyce. “There seemed to be two roles played by women: femmes fatales, driving men to their deaths, or figures of beauty in quiet contemplation, but without being active agents.” The gallery in which Hylas and the Nymphs hangs is titled, without irony, “the Pursuit of Beauty”.

Conversation kept coming back to this work, Waterhouse’s 1896 vision, inspired by a poem by Theocritus, of semi-naked girls luring Heracles’s beautiful young lover into a lily-bedecked pond. They are complicated creatures, those nymphs: sexually voracious and destructive; beautiful and powerful; objects of titillation for the implied heterosexual male viewer; presumably modelled by some rather young girl, or girls. The work hangs opposite Charles-August Mengin’s painting of a young, tragic Sappho, bare-breasted, about to hurl herself from a cliff in grief at her unrequited love for a man. (This story about her death circulated in antiquity, and gained a certain popularity in the 19th century, though the internal evidence of her poems suggests she lived into old age.)

Cheddar Gorgeous’s performance. Photograph: Sonia Boyce

The conversations in the museum registered that both paintings featured classical characters famous for homosexuality – a homosexuality completely invisible in these works. Gallery attendants noted that young girls often took selfies with Hylas and the Nymphs as backdrop, and that middle-aged men also liked to linger over it. “There were rich conversations over a number of months,” says Boyce. “What has got lost from the subsequent discussion is that what I do involves a process.”

There is another part of the way that Boyce works that provides some of the backstory to the removal of Waterhouse’s painting. Her art, over the past decade or so, has often involved bringing apparently disparate ingredients together and, without interfering or directing too much, watching them react – and then using footage of these encounters as material for a film work of her own. For example, for Exquisite Cacophony (2015), a work that will be on show in her retrospective, she asked the (white, American, southern) rapper Astronautalis and the (black British) experimental vocalist Elaine Mitchener to make an improvisatory performance together at the Victoria and Albert Museum, London.

The event began with Astronautalis chuntering away with a mic on a stage, performing something like a stream-of-consciousness standup routine. Mitchener began to disrupt his monologue with whoops, whistles and cackles, so that the event became a sometimes irritable confrontation between two artists from apparently completely different traditions. In the end, though, the confrontation eased. The two reached an accommodation, and even, in a gently symbolic moment, swapped shoes. The two artistic worldviews, it became clear, are not so oppositional after all. They are contaminated by each other, and they were entangled all along.

Boyce did something similar in Manchester. The conversations with staff and volunteers were to culminate in an evening “takeover” event in the 19th-century galleries on 26 January. It had been decided by participants in the debates that the evening would include the unscrewing of Hylas and the Nymphs from the gallery walls, to be replaced by a blank space on which a series of questions would instead be displayed, inviting responses from the public.

But that was only one element of the evening. Prompted by the questions of sexuality and gender raised by works in the galleries, and of race, and of performing and cross-dressing – the portrait of Ira Aldridge having set in motion thoughts about Shakespearean transvestism – Boyce invited a group of drag artists, and the queer actor and writer Lasana Shabazz, to perform in the galleries during the evening. Venus Vienna, standing in front of Hylas and the Nymphs, handed Polaroid selfies – some of them uncomfortably intimate – to passersby. Liquorice Black was costumed as the dark, hooded Sappho of Mengin’s painting, and scribbled away furiously, never speaking. Cheddar Gorgeous created an ingeniously scanty costume to reference another Victorian vision of naked female flesh, Charles Roddam Spencer Stanhope’s Eve Tempted (1877).

The evening was one of “masquerade, dressing up, acting up, humour and anxiety”, says Boyce. It was not just about taking Hylas off the walls; it was also about making gender mischief in the galleries. She has constructed her video work Six Acts from footage filmed that evening. Not everyone will like it, she thinks. “Some people might be offended – it might be seen to have been disrupting the calm of the galleries.” At the very least, one participant at the “takeover” evening was unhappy: it was a painter called Michael Browne who, worried about implications for artistic freedom, posted on Twitter and the gallery’s website, and was quoted by the press after Hylas and the Nymphs was taken down.

Lasana Shabazz at the takeover. Photograph: Sonia Boyce

Boyce is clear that she is not about to start recommending that the entire history of western art – with its thousands of acres of titillatingly displayed female flesh – be removed from our museums and galleries. On the other hand, she does insist that the past is not, as she puts it, “sealed off” from the present. We have a live relationship with it, one that changes and develops, and sometimes becomes fraught.

Feminist critiques of artists’ portrayal of female flesh are nothing new: in 1972, John Berger devoted a programme to just that in his watershed BBC series Ways of Seeing, and artists, curators and historians have been tackling the question of the male gaze since film critic Laura Mulvey coined the term in 1975. (This continues: in the BBC’s Civilisations, Mary Beard considers the curious history of what might have been the first female nude sculpture of antiquity, Praxiteles’ Aphrodite – over which, or so the story goes, an early fan became so obsessed that he ejaculated on it.)

Nor do paintings arrive on museum walls by magic. Someone decides to put them up – and, later, to take them down or move them around, which is the job of a curator. This might happen for all kinds of reasons, including the changing of taste or, indeed, a shift in the limits of acceptability. One thinks of the fig leaves that sprung up over the genitals of classical statues in the 19th century, or the “secret cabinets” where phalluses and other formerly unacceptable objects were once placed in museums.

Consensus rarely remains stable: in December, a petition was got up to try to persuade the Metropolitan Museum of Art in New York to remove a 1938 Balthus painting of a prepubescent girl posing in a provocative position (the museum left it up). Hylas and the Nymphs was removed through an impulse to reveal normally hidden institutional machinery to the public, and to invite them to take a stake in it.

It is an open question whether removing Hylas and the Nymphs was a good idea. Many still believe it was ill-judged at best, and that its removal amounted to censorship even if it was not intended as such. Some would say, if you want to have a conversation about Hylas and the Nymphs, keep it in view, not locked in the store. Others would argue that the picture has been looked at and thought about more productively since its brief disappearance than it has for years. Like it or not, the act provoked questions about how we relate to the past, and to its art, that are not going away.

The Sonia Boyce retrospective is at the Manchester Art Gallery from 23 March-22 July, free, manchesterartgallery.org

• This article was amended on 19 and 23 March 2018. Sonia Boyce became the first black female Royal Academician in 2016, not 2008 as we had it. In addition, an earlier version said that with the Tate’s purchase of Missionary Position II in 1987, Boyce was the fifth woman to enter the collection. In fact by the end of 1986, Tate had 212 women artists.

