Cardiff is hosting the fifth annual Welsh Amateur Operatic Contest, and choirs, singers and soloists are practising all over the city. A small choir rehearsing at the Church of St Emmanuel is attacked by something wrapped in a silence so profound that it swallows all other sounds in its vicinity; a six-year-old girl named Kate Healey who lives near the church is traumatised simply by the unseen creature's passing by her house. Torchwood is called in to investigate, and DI Tom Cutler is perfectly willing to leave the strange case to Gwen and Jack; he's encountered Torchwood before, under circumstances that led to him being transferred to Cardiff from Hammersmith. Whatever attacked the church smashed through its stained-glass window and killed one of the singers, Richard Greenwood of Newport; his body has been sliced open, his clothing is fused to the skin near the wound, and his vocal cords have been removed without damage to the surrounding tissue. The other four members of the choir are in hospital, suffering from extreme trauma brought on by a sense of isolation so deep that they become hysterical just thinking about it. Shocked by the depth of their suffering, Gwen vows to dose them all with retcon as soon as she can.
Dyllis Llewellyn and her husband Barry have competed in the contest for the past four years, but Barry will be singing solo this year, as Dyllis suffered a stroke and is no longer able to sing. Privately, she suspects that Barry is pleased by this turn of events, as she was always the weaker singer. A tyre blows out on their car as they near Cardiff, and Barry begins to sing while repairing it; however, Dyllis senses something silently watching them and is gripped by a sense of terror. Panicking, she interrupts Barry and urges him to finish his work; he does so, and they continue on to the Bay View Bed and Breakfast. Unfortunately, Barry begins singing in the shower the next morning, and the thing that killed Richard Greenwood smashes through the window and kills him as well. Dyllis suffers a second, more massive stroke upon seeing his body. A woman named Karen Peters is also killed while singing in the restrooms at her workplace, Cooper Drake Insurance. News of the murders soon reaches the press, who begin hounding DI Cutler for answers. At the Hub, Jack sends Ianto and Gwen home to rest while he works through the night; this turns out to be a good move, as the isolation and silence of the empty Hub reminds him of a legend he'd once heard.
Meanwhile, a barrister named Adrienne Scott visits her son Ryan at the Havannah Court Autistic Centre. Ryan spends his every waking hour singing, and Adrienne used to believe that his beautiful voice was proof that something deep inside him was trying to reach out to her, until her husband Michael forced her to listen properly to Ryan and she realised that he was perfectly reproducing the songs that he'd heard on CD. The revelation destroyed her marriage, and although she visits Ryan three times a week, she's only going through the motions and considers herself a terrible mother. Ryan's nurse, Ceri Davies, seems to genuinely care for the boy, but Adrienne doesn't believe that she still loves her son.
That night, the Milford Haven Women's Institute has a close shave with the creature while rehearsing in the Llandaff community centre. Musical director Annalise George is alienating the singers by trying to claim too much authority, and when star soprano Alice Jones suddenly stops singing out of a sense of foreboding, the others decide to take a break. Later, when they leave the hall, they notice a broken window in the back. Elsewhere, diva soprano Maria Bruno -- born Mary Brown in the Welsh Valleys -- arrives at the five-star St David's Hotel with her milquetoast husband Martin Meloy, whom she privately despises. She and Martin have separate rooms at the hotel, and once she's alone in her suite, Maria takes a moment to appreciate the beauty of Cardiff from her balcony. Moved, she begins to sing Ave Maria, and the creature comes for her. Later that same night, singing duo Ben Pritchard and Drew Powell run into their singing rivals, working-class thugs Tony Lockley and Angus Parker, at a pub. The flamboyant Drew responds to their homophobic taunts with mockery, and Ben, upset with Drew for ruining his quiet night out at the pub, argues with his partner and leaves the pub without him. Alone on the streets, Ben sits in an empty children's playground on Angel Street and tries to calm himself down by singing.
The next morning, Gwen's pleasant night with Rhys is ended when Ianto calls with news of two more murders. The high-profile death of Maria Bruno puts more pressure on both Torchwood and DI Cutler, and Gwen is upset that the authorities seem not to care about the other victims such as Ben. However, Jack believes that he knows where the creature comes from. According to legend, there is a world called the Silent Planet near the edge of the known Universe, and its inhabitants are incorporeal and spend their lives in silence and isolation, taking form only to mate. If one of these creatures has fallen through the Rift, perhaps the noise and commotion of this world has driven it mad. Jack sends Gwen to enlist Cutler's help in setting a trap for the creature, as Cutler is the public face of the investigation and Jack believes that Torchwood owes him a favour after their last encounter.
Drew Powell arrives at the police station at the same time as Gwen, desperate for news about the investigation. He vows to sing alone in the competition in Ben's memory, and Gwen, inspired, asks Drew to help set a trap for the killer. Cutler is reluctant to involve a civilian, but Drew insists upon helping. Since Ianto used to sing as a youth, he becomes Drew's temporary singing partner, and they practice together at St Jude's, a church near the epicentre of the killings, while the others wait outside. Frustrated by Ianto's lack of passion, Drew demonstrates how to do it properly by singing a solo aria, putting all of his grief into the song. Outside, Gwen detects multiple energy spikes converging on the church, and she, Jack, and Cutler rush inside just as a dark humanoid figure smashes through the window and attacks Drew. Ianto tries to trap it in a portable force field, but the creature knocks him aside as it passes by. Jack shoots the creature, driving it off before it can complete its work, but Drew has been badly injured. Gwen and Ianto take him to the hospital, and once they're sure that he's going to survive, they dose him with retcon; he will still have to cope with his injuries and the loss of Ben, but not with the terrible sense of loneliness and isolation that Ianto felt radiating from the creature.
Jack takes Cutler out for a drink and a chat, curious to know what drove Cutler to act as he did during his last encounter with Torchwood. Cutler explains that while staking out the home of suspected paedophile Mark Palmer, he saw for himself that a glowing white light had possessed Palmer and was driving him to commit atrocities against children's dead bodies. Cutler stumbled across Torchwood while trying to find an organisation that dealt with this sort of thing, but while they took care of the entity inside Palmer, they did not intervene when Palmer was arrested and charged with the crimes the entity had forced him to commit. Aware that Palmer was not really responsible for what he'd done, Cutler lied on the witness stand, claiming to have planted DNA evidence to ensure a conviction. Cutler's career and marriage were destroyed by the lie, but Palmer was kept out of prison, even though he eventually ended up in an asylum.
Haunted by his recollection of these events, Cutler lashes out at the banal music in the pub and wishes for a few moments of peace and quiet -- which gives Jack an idea. Back at the Hub, he explains that he's going to ask the contest judges to call for two minutes in silence in memory of the murder victims; during that time, Ianto will sing a solo and lure the creature into a trap. Gwen and Ianto have refined the Rift monitors to give them more warning of the creature's approach. Ianto adds that he felt a terrible sense of loneliness when the creature attacked Drew; perhaps it isn't driven by anger, and doesn't understand that it's killing its victims. As the team prepares to set their trap, the alien is waiting elsewhere in the city, aware that it doesn't have long to take what it needs; Ryan Scott is sleeping peacefully at the Autism Centre while Adrienne drinks herself to sleep at home; and Martin Meloy is committing suicide, unable to face life without Maria.
The next morning, Gwen remains at the Hub to monitor the Rift while Ianto, Jack, and Cutler set the trap at the Church of St Bartholomew. The contest judges have agreed to declare two minutes of silence, but as the hour approaches, Cutler sees a student named Nina Rogers walking down the street, singing along to her iPod; he stops her and sends her back home. Gwen then reports that the Rift spikes are appearing -- but they're converging on the Havannah Court Autistic Centre rather than the church. The Torchwood operatives and Cutler rush to the Centre, where the hung-over Adrienne has arrived to visit her son, who hasn't stopped singing since he woke up. She notices movement in a tree outside the window, and Ceri leaves to determine whether a child has wandered out of the centre; the creature then coalesces out of the air by the tree and rushes straight for the window. Like its other victims, Adrienne experiences a crushing sense of isolation and despair -- but when her personality is reduced to basics, she realises how much she really loves her son, and she plants herself between Ryan and the creature, refusing to let it past.
Cutler and the Torchwood operatives arrive as the creature smashes through the window, killing Adrienne. But unlike the creature's other victims, Ryan doesn't stop singing at its approach. To Ceri's astonishment, Ryan reaches out for the creature; this is the first time he's ever acknowledged the existence of something other than himself. Seeing the boy and the alien together, Jack realises that the alien suffers from the Silent Planet's counter-equivalent of autism; just as Ryan craves isolation in a noisy world, the creature craves contact with others. Attracted by the beautiful music on this side of the Rift, the alien has been taking the physical parts that created the music, unable to understand that it was the emotion and the process of singing that was important. Jack realises that the boy and the alien can complete each other, and decides to let them bond and depart in peace. Gwen isn't sure that this is the right thing to do, but gives in when Ceri agrees, pointing out that the boy's father never comes to visit him and that his mother is now dead. Ryan and the alien merge into a single entity, and the Rift then opens up and transports it back to the Silent Planet; the alien is no longer alone, and Ryan will never be bothered by the outside world again.
Cutler calls the police to the latest crime scene, and plants DNA evidence framing Martin Meloy for the killings. The official story will be that Martin snapped after years of abuse from his demanding wife, killed her after practicing his technique on other innocent victims, and committed suicide upon realising that he was too caught up in the bloodlust to stop killing. Cutler notes the irony; having destroyed his career by falsely claiming that he'd planted evidence to frame an innocent man, he's now restored his career by doing that very thing. He chooses to remember the truth about what he's done, but Jack slips him some retcon anyway, feeling that it's too dangerous to have him wandering about with knowledge of Torchwood; when Cutler awakens, he will believe the official story that he's redeemed his past offences by catching a serial killer.