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On the day that the U.S. government relaxes wartime restrictions and allows tugboats to return to work, Alec Severn, the proprietor of Secoma Towing & Salvage, desperately searches for Tugboat Annie Brennan, the captain of his fleet. Wanting to replace Annie, his longtime nemesis, rival captain Bullwinkle gives Severn an incorrect address for Annie. The indomitable Annie nonetheless reaches Severn's office just in time and signs a new contract with him. Annie then hires her crew, all of whom are veterans: Pinto and Shiftless, who worked with Annie before the war; a newcomer named Missouri Jones; and Johnny Webb, who was injured while saving the lives of the other three men in combat. Soon after Annie begins work with her crew, they are interrupted by the appearance of Susan Henley, an orphan whose father used to work for Severn. Susan, a violin prodigy, wishes to stay with Annie, who wants to adopt her, but Severn convinces Annie that Susan would be better off living with his family. Annie still pines for a child, however, so Severn arranges with Judge Abbott for her to adopt one of the juvenile delinquent boys under his jurisdiction. On the day of her "son's" arrival, Annie is dismayed that the "boy" sent to her is Terry Jordan, a young veteran on probation for beating the man who swindled Terry's now-deceased mother while he was fighting overseas. The hostile Terry rejects Annie's friendly advances, and his treatment of Annie does not endear him to her crew either. Later, Annie and Marion Graves, Abbott's secretary, arrange for Susan to make her debut with famed conductor Alfred Puccini, a womanizer whom Annie knew when he was the ordinary Al Pucci. In order to prevent Pucci from discovering that Susan is only eleven years old, Annie convinces him to wait to meet his new "protegee" until the night of the concert. As Susan rehearses, Annie and her men work hard, although Annie continues to feel hurt by Terry's rejection. One day, after learning that Severn has given Annie an important assignment, Bullwinkle empties her fuel tanks and disables her radio so that he can steal the job. The crew mistakenly believes that Terry is responsible for the sabotage, and Johnny challenges Terry to a fistfight. Terry beats Johnny until he sees Johnny's leg brace, and after he allows the disabled man to win the altercation, Terry invites the other crewmen to get their licks in. Having won the men's respect, Terry then forces Bullwinkle to admit that he committed the sabotage. Annie's faith in Terry is restored, but he disappears before she can reconcile with him. He leaves behind a note apologizing for his behavior and promising to return someday. Although she misses Terry, Annie gladly attends Susan's debut, during which the amazed Pucci is so impressed with her talent that he forgets the trick played upon him by Annie. After the concert, Annie and her crew return to the waterfront, where they immediately help battle a fire started by a welder. Terry has also returned and pitches in to help, as does Bullwinkle. As Annie's tug tows a blazing oil tanker away from the wharf, Johnny sacrifices his life to save Terry, who was attempting to free the tanker from Annie's boat. Afterward, Annie wants to quit, but Severn assures her that her bravery and that of her men has won them a lucrative contract. Terry, who has just married Marion, also asks Annie to stay, and finally embraces her and calls her "Mom." Susan is set on the road to stardom with a contract with the San Francisco Symphony Orchestra, and Annie playfully reconciles with Bullwinkle, who dives into the water rather than accept a kiss from her.