It was time Billy came home. The Flying Dutchman puts in to shore every seven years, but the HMS Indomitable hasn't dropped anchor at Covent Garden in nearly two decades. The Royal Opera presented the 1951 premiere of Britten's Billy Budd, and its two-act revision, but it's been 19 years since the able seaman last scaled the rigging in Francesca Zambello's 1995 staging. Deborah Warner's new production has already travelled many nautical miles, enjoying successful runs at Madrid's Teatro Real and the Teatro dell'Opera di Roma, each house – incredibly – performing Budd for the first time.

“I am an old man who has experienced much.” Although nearing 50, Toby Spence still looks fresh-faced enough for Captain Vere's opening line to raise an eyebrow. But here “Starry Vere” appears in both prologue and epilogue alongside an aged version of himself, an elderly man with a haunted, faraway look, perpetually scouring the deck – holystoning – with a Bible. Warner doesn't push the homosexual overtones in the opera, but highlights the work's religious and redemptive power, seeing it as a parable of good and evil, but with all the ambiguities that can be read into parables.

Warner writes of John Claggart, the master-at-arms who destroys Billy with his false accusation of inciting mutiny, as “a fallen Angel”. Fresh-faced Billy is an innocent, a lamb to be slain, hands manacled, nuzzling into Dansker's back when the old seadog brings him a sip of grog and a biscuit – a clear allusion to the Eucharist – before his execution. The most telling scene comes after the drumhead court martial sentences Billy to hang. Usually, Captain Vere heads off-stage to deliver the verdict, but Billy is present throughout, turning the scene between the two men, played out over Britten's astonishing sequence of 34 chords, which start crushingly but gradually dissolve, into something very powerful. As Billy climbs down into the hold, he places his palm on Vere's forehead, absolving him. It's a moment that chokes.

Michael Levine's semi-abstract set of floating platforms is flanked by rigging of hundreds of ropes, dangling like prison bars. The split staging is effective when Claggart delivers his Iago-like Credo just a few feet above Billy, slumbering below decks. However, those in the upper reaches of the house may have found this raised deck obscured their view of Billy's prison scene. Chloe Obolensky's sharp naval uniforms seem to place us in the Second World War – HMS Indomitable was also the name of a 1940s aircraft carrier – although the sixty hammocks suspended below reference the man-of-war war frigate of Britten's original 1797 setting in the Napoleonic wars. Despite the wide expanse of the staging, Jean Kalman's evocative lighting creates an oppressive, claustrophobic atmosphere. The only miscalculation is a sharp blackout at the end which invites applause far too soon; it cries out for a soft, silent fade-out.

The central trio is sharply etched. The athletic Jacques Imbrailo is a seasoned Billy, familiar to Glyndebourne audiences. Here, his ash baritone didn't always gleam easily at the top, but emotionally he digs deep. “Billy in the Darbies” was hugely affecting due to the almost broken-voiced delivery. Brindley Sherratt is outstanding as a cold, bespectacled Claggart, his Credo oozing satanic blackness of voice. “I will destroy you” is followed by sleaziest saxophone solo, but Sherratt doesn't portray Claggart as an out-and-out villain; this is a nuanced performance. Claggart's goading of the stammering Billy during his accusation means the fatal blow that fells him is more convincing than usual.

Warner makes Vere's moral dilemma the central key. Toby Spence's captain is remote, a dreamer reading Plutarch in his bath, pressing his ear to the deck as the crew sing shanties below, lulled into believing his men are content with their lot. Spence was in terrific voice, able to float honeyed head notes but his tenor rings out like a bell in Vere's more declamatory moments. He clearly knows Claggart is dishonest but is too bound by rules to speak up for Billy, a Pilate-like figure who neglects to save an innocent.

The rest of the Indomitable's crew is similarly top notch, from Clive Bayley's salty Dansker, Duncan Rock's muscular Donald and Sam Furness' fresh-voiced Novice below decks up to David Soar's steely Mr Flint and Thomas Oliemans' fine Mr Redburn, officers mocking the hoppity-skippity French. Many of this crew have sailed with this production from its Madrid premiere in 2017, including conductor Ivor Bolton, General Music Director of the Teatro Real. He mostly balanced voices and orchestra well – although it wasn't the most distinguished night for the brass – and drove the pulsating “This is our moment” rallying call boldly, the men of The Royal Opera Chorus shaking the rafters. A powerful, often devastating performance.