While travelling by train with his sidekick and assistant, "Goldie" Locke (Edward Brophy), for a vacation in San Francisco, Tom Lawrence (Tom Conway), a.k.a. The Falcon, meets Annie Marshall (Sharyn Moffett), a lonely little girl. Annie tells them that she is being held prisoner by her nurse, Miss Carla Keyes (Hermine Sterler), and butler Loomis (Jason Robards Sr.). Annie's story is cut short when Miss Keyes comes for her. Shortly after, the little girl rushes back to Tom to tell him her nurse is dead.
Tom and Goldie take charge of Annie but police are notified that the little girl was kidnapped. When the train arrives in San Francisco, the police are waiting for the Falcon. Released on $10,000 bail, posted by Doreen Temple (Fay Helm), who promises Tom she will disclose the motive behind her generosity. At dinner that evening, Doreen brings along her bodyguard Rickey (Carl Kent), posing as a police officer. When they leave, Rickey knocks Tom out and takes him to Doreen's apartment where she interrogates him about the murder, and to stay away from gangster Peter Vantine (John Mylong) and the cargo ship, the S.S. Citadel.
After Tom returns to his hotel to collect Goldie, they decide to pay a visit to Annie's house, where they meet her older sister Joan (Rita Corday) who denies that she knows Doreen or Vantine. Annie claims she made up the story about being held captive, but when Tom sneaks back to the house to talk to her, she says Loomis is holding her prisoner. She takes them to Carla's room where they find a photograph of a ship's officer (Johnny Strong), signed to his wife, Carla.
Loomis hears someone rummaging around in the nurse's room, but is shot dead by an unknown assailant. Returning to their hotel, Tom is confronted by Vantine, who is brandishing a gun. When Tom disarms him, he learns Doreen was the romantic interest of an ex-bootlegger, Duke Monette (Robert Armstrong), involved with a shipment aboard the S.S. Citadel.
Tom visits the Star Coastal lines where DeForrest, the company's general manager is meeting with Joan, the owner of the company. A call at the office, alerts Tom to go to an address, which turns out to be Doreen's apartment, where she is waiting with her gang. Vantine, also lured into her trap, arrives and begins to fight with Doreen's thugs. Tom and Joan manage an escape but on his return to his hotel room, discovers DeForrest hiding in a closet. Goldie finds a newspaper article that shows who the real owner of the steamship S.S. Citadel, is Duke Monette.
That night Tom and Goldie sneak aboard the ship and find raw silk hidden among the bales of hemp cargo. Returning to the Marshall house, the little girl tells Tom, that Joan has left to meet her "secret lover" on Telegraph Hill. Tom observes the rendezvous with Joan and DeForrest, who Tom thinks is really Duke Monette, confessing that he used a secret identity to protect his daughters, Joan and Annie.
Fearing Doreen plans to hijack the illicit silk cargo that night, Duke asks for the detective's help. At dockside, Duke and Tom watch Vantine, Doreen and the other gang members board the S.S. Citadel. Duke suddenly knocks the ship's engineer unconscious, and blows up the unattended boiler room, then pulls a gun on Doreen and Tom.
Tom tells Doreen that Duke killed Miss Keyes and Loomis, the employees she hired to watch over the girls. When Tom warns that Duke plans to blow up the ship, Doreen and Rickey lunge forward to disarm Duke, who shoots them both, but Rickey shoots Duke, allowing Tom to flee before the ship explodes.
"My Shining Hour" (1943) (uncredited) and "The Sky's the Limit"(music only), music by Harold Arlen, lyrics by Johnny Mercer was played by house orchestra in the nightclub scene. Sequences in The Falcon in San Francisco were shot on location at prominent locations in San Francisco.
Film historians Richard Jewell and Vernon Harbin described The Falcon in San Francisco, as part of a programmed series. "One of the quaint conventions of the Falcon series was that whenever Tom Conway embarked on a vacation, a corpse would pop up to interrupt his relaxation".
In a recent review of the Falcon series for the Time Out Film Guide, Tom Milne wrote, "Conway, bringing a lighter touch to the series (which managed its comic relief better than most), starred in nine films after The Falcon's Brother, most of them deft and surprisingly enjoyable." After its release into home video, The Falcon in San Francisco was reviewed in DVD Active.com, "The plot gets thicker than Northern gravy with boiled potatoes when more bodies hit the sawdust, and links to a shipping magnate are uncovered - all linked to a man with no past and a gangster thought to be long dead. Will The Falcon unravel this mystery without taking a bullet? Will the mafia have their plan thwarted? Can Goldie find himself a bride to reduce his level of income tax?"