Your Black Muslim Bakery had been an Oakland institution for decades, a business and community organization rooted in a mosque founded by the elder Yusuf Bey. By 2007, the bakery was on the verge of bankruptcy, and Bailey was investigating its finances. He had a source inside the organization, a former employee named Ali Saleem Bey, who told him the bakery had been seized from its rightful heirs through fraud and forgery by a younger branch of the family. The Oakland Post's publisher, Paul Cobb, had already withheld an earlier version of Bailey's story from publication, saying only that it concerned matters similar to what eventually happened to Bailey. Cobb later said police had asked him to keep quiet. The story Bailey was working on when he died would have exposed how Yusuf Bey IV, the bakery's young CEO, and his associates had taken control of the organization through forged documents and intimidation.

The elder Yusuf Bey had fathered forty-two children by different women before his death in 2003. What he left behind was less an inheritance than a power vacuum. His son Antar Bey seized control of the bakery and took out $700,000 in loans to cover back taxes and debt. When he defaulted, foreclosure loomed. Then, in October 2005, Antar was killed in a carjacking in Oakland. Authorities suspected Yusuf Bey IV of ordering the murder but could never prove it. By the time Bailey began his reporting, Bey IV had accumulated a record that included theft by deception, forgery, fraudulent loan applications, and a bizarre kidnapping in which he and four associates abducted two women, blindfolded and beat them, and demanded money. He was twenty-one years old, and he ran the bakery like a criminal enterprise because that is what it had become.

Broussard had been rehired at the bakery in July 2007 after a stint away. The night before the murder, he went looking for Bailey at his apartment complex near Lake Merritt. Early the next morning, he tried Bailey's office, but the editor had not yet arrived. So Broussard waited along Bailey's regular route. The killing was not subtle. Witnesses reported at least three shotgun blasts on a downtown Oakland street in broad daylight. Broussard later confessed, telling investigators he was following orders. At trial, he testified that he carried out the murder and another killing, that of Odel Roberson, "because Yusuf Bey IV told me to." A third murder, the random shooting of a chef named Michael Wills, was carried out by another bakery associate, Antoine Mackey, during a drive through Oakland in which the men had been discussing the 1970s Zebra murders. Mackey shot the unarmed Wills six times.

Almost two years passed before a grand jury indicted Bey IV for ordering Bailey's execution, along with the murders of Roberson and Wills. The trial, which began in 2011, was marked by relentless witness intimidation. Former bakery followers who had given statements to police changed their stories on the stand or claimed memory loss. One convenience store worker said he could not remember more than fifty times during his testimony. A jailhouse videotape captured Bey IV whispering details of Bailey's murder to his half-brother and an associate, footage the Chauncey Bailey Project, a coalition of journalists formed to continue Bailey's work, obtained and published. In June 2011, Bey IV was convicted on three counts of first-degree murder and sentenced to life without parole. Mackey received the same sentence. Broussard pleaded guilty to manslaughter in exchange for a twenty-five-year sentence and full testimony. He was released on parole in 2025. In 2013, Bey's own attorney was convicted of smuggling a hit list out of jail on his behalf.

Bailey's fellow journalists did not let his work die with him. The Chauncey Bailey Project brought together reporters from competing outlets to investigate both the murder and the bakery's finances, the very story Bailey had been killed to suppress. Their reporting helped build the case that led to convictions. The project stood as a rare example of collective journalism driven not by competition but by principle: a reporter had been murdered for doing his job, and the profession closed ranks. Bailey had spent decades covering Oakland's African American community for outlets including the Oakland Tribune and the Detroit News before joining the Post. He was not an investigative reporter by training. He was a local journalist who followed a financial story to its logical conclusion and discovered that the people he was writing about would rather kill him than be written about. His death exposed how thoroughly a criminal organization had embedded itself in a community institution, and how long Oakland's systems of oversight had failed to intervene.