Two smugglers are surprised by a harbor policeman, and shoot him down.Baxter gets to him, an old friend, in time to hear his last words, "Camphor Tubes". He soon realizes this is the method of hiding contraband the killers are using.
When Captain Hardesty fires an electrician for constantly picking fights with his fellow crew members, the enraged sailor threatens to blow the vessel into smithereens. Hardesty thought nothing of the threat until he discovered detailed plans to build a time bomb and reports his fears to Harbor Command. Captain Baxter and his men try to locate the crazed sailor before he can complete his bomb full of nitroglycerin.
When police break up a craps game, one of the arrested men is found to have two counterfeit $20 bills in his pocket. The Harbor Command and the Treasury Department track the money through seaman slated to leave port that day for Hong Kong to a pawnshop owner who claims to have never met the seaman.
A small-time shipping company also helps smuggle diamonds for a gangster. When the shipper-turned-smuggler's brother finds out, he threatens to call the police, and is killed in a fight. Guilty over the murder, he wants to confess, but the gangster threatens his girlfriend.
Captain Baxter and his men respond to report of a disabled fishing boat and discover that old Pop Cates has run out of gas for the third time in a month. Baxter learns that Pop's daughter has canceled her visit and the elderly fisherman is distraught because he has never seen his six-year-old grandson and fears the worst when the leaky vessel is spotted heading for the open ocean.
Captain Baxter and Sergeant Warren investigate the murder of night watchman on one of San Francisco's piers. They discover a map covered with oriental writing and learn that it marked the spot where Japanese smugglers hid $100, 000 worth of gold bars just before World War II. When a merchant seaman is discovered fatally stabbed, the Harbor Command officers find a clue to the killer.
Captain Baxter is asked to go undercover to follow a lead developed by a U.S. Treasury agent who murdered after gaining the information about a counterfeit ring. He travels to Los Angeles and attempts to follow counterfeit plates from one crook to another until they reach the head of the syndicate.
Harbor Command and the San Francisco Fire Department match wits with an arsonist that causes a false alarm at one waterfront location, then sets another conflagration while the fire equipment is concentrated miles away from the real fire. Captain Baxter devises a plan to trap the firebug with fake bags of nitrate.
When 4500 sailors from a U.S. Navy carrier task force return to port with six months of back pay in their pocket, they are ready for shore liberty - and the crooks and con men are waiting for them. The Harbor Patrol request assistance from the Navy's shore patrol when a sailor is stabbed in a bungled robbery and it appears that the crook are planning to dispose of the wounded man in the Pacific Ocean.
Harbor Command investigates the report of a derelict fishing boat floating in the middle of San Francisco Harbor. They quickly discard their initial theory of insurance fraud when they discover human blood in the cockpit and a check for $10,000 missing from the captain's cabin. Captain Baxter and Sergeant Warren's investigation focuses on the individual crew members and learn the first mate was new to the vessel.
A waterfront bum spots a young couple throwing a young man into the San Francisco harbor, but is afraid to report it to the police because he was supposed to be covering for the night watchman who was playing poker. When the tycoon's death is reported in the newspaper, the watchman and the bum use the couple's license plate to trace the murderers and blackmail them. Meanwhile the harbor command investigates the murder.
A teenage girl sneaks out of her father's house for an assignation with an older man. While the couple are making out, an armed robber sneaks up beside their car and kills the young man when he refuses to give the crook his wallet. Fearing her father will punish her for seeing the young man over his objections, the teenager refuses to assist the Harbor Command with their investigation. Listening to the police radio band, the crooks learn the girl's identity and determine to eliminate the witness before she changes her mind.
Captain Baxter receives a tip that a gang of lobster smugglers might be behind the murder of an ex-convict found floating in San Francisco Bay. After discussing the matter with state fishing personnel, Baxter decides he's searching for bigger game - a deported criminal seeking to reenter the country illegally on board a small fishing boat.
A recently released convict won't forget that it was Baxter that had him sent up, and now determined to exact revenge with a high powered rifle he steals from a gunsmith's shop. He taunts Captain Baxter with phone calls to his office, takes a shot at him at his apartment, and follows him to a highly public meeting, concealing the gun in a brief case.
Captain Baxter and Sergeant Warren respond to a call from a hotel clerk who states he was beaten by a boarder, who had also ruined his bed with repeated knife thrusts. The Harbor Patrol learns that the perpetrator was Leon Faulkner, a former convict recently released from prison who harbored a grudge against the psychiatrist who testified against him at the convict's trial ten years earlier.
When Captain Baxter learns a freighter from a communist country that docks in San Francisco to make emergency repairs he decides to pay the ship's captain a visit. He discovers that a famous scientist used the visit to seek asylum in the United States. Fearing the police and the communist operatives who are pursuing him, the scientist desperately tries to reach a street mission where he had been advised to seek sanctuary. Baxter and his men try to reach the scientist before he comes to harm.
Two armed robbers, one of whom was wounded during a shootout with a watchman, hijack a San Francisco Bay water taxi and force the passengers to hide them on a yacht in the marina. Fearing for the safety of the hostages, Captain Baxter masquerades as the vessels owner so he can climb aboard to affect a rescue.