While searching McHale's island for a stolen case of rare champagne, Binghamton captures Fuji, and places him under arrest, as a spy. McHale and The Crew must then concoct a complicated plan to free their Japanese friend, which not only succeeds, but winds up with an unexpected bonus.
Binghamton begins to regret having so harshly punished the 73 Crew, when McHale and The Boys - While in the process of trying to rid their island of a bothersome bird - Give The Captain the impression that they are out to get even.
Binghamton accuses Parker of cowardice, after Parker loses his cool, during the pursuit of a Japanese patrol boat. But Parker redeems himself, when - After a little pep-talk from McHale - He orchestrates the destruction of a German U-Boat, on a mission to rendezvous with a Japanese patrol.
McHale and The Crew devise a plan - Potentially beneficial to both them, and Captain Binghamton - To have a popular movie star put on a show on Taratupa, for Admiral Rogers, but must first scheme to get the Star's stubborn Tour Manager out of the way.
In an attempt to impress an Admiral, Binghamton drops some serious charges against the 73 Crew, in return for a show of their 'high esteem' for their Commander, in the form of a testimonial dinner. Knowing that no one will attend the dinner willingly, McHale and The Boys plan to combine the dinner with a big crap game, in order to have a showing for the most hated Commanding Officer in the Pacific.
McHale and The Boys have planned some entertainment for the Base Personnel, but Binghamton puts a stop to it, and orders McHale and his Crew to ferry him to a Staff Meeting, so that he can keep an eye on them. But, after the 73 is put out of commission by a Japanese plane, Binghamton if forced to do some entertaining of his own, during a mission to obtain some fuel, on a Japanese-held island.
While trying to impress a pretty Nurse, Parker receives several serious blows to his morale, and, humiliated, he puts in for a transfer. Then, complications arise, when McHale, The Crew, and the Nurse work up a plan to try to help him to regain his self-esteem, and change his mind.
When Binghamton finds out that Parker is an old friend of a famous War Correspondent, he makes Parker the Base PR Officer, in the hope of becoming the subject of the Correspondent's next story. But Parker's plan to improve The Captain's image backfires.
Gruber and the guys concoct a very tall story, to try to turn Tinker into a hero, so that he can win the heart of his favorite girl. But, the rumor of Tinker's 'Secret mission' soon spreads throughout the South Pacific, and trouble develops, when glory-hungry Binghamton tries to get in on the action.
Binghamton is convinced that McHale and the 73 Crew are consorting with the enemy, and, when he can't get anyone to believe him, he calls for a Naval Intelligence team, to search McHale's island for evidence. So, to get him to call off the search, McHale and The Guys devise an elaborate scheme, to make Binghamton think he's losing his mind.
While on an unauthorized liberty, in New Caledonia, McHale and The Crew are all thrown in jail, for various reasons, during which time, a crooked Frenchman steals the 73 to use for some crooked business. McHale and The Crew must then scheme to get out of jail, find the crook, and get the 73 back, before Binghamton returns from a Staff meeting.
When Happy begins sleep-walking, due to his insecurity with women, Binghamton orders him to be psychiatrically evaluated, and shipped out, if found unfit for duty. So, McHale and the guys try to help their Shipmate, by fixing him up with a pretty Nurse, but must first get around Binghamton's 'No Fraternization' rule.
The 73 Crew's heart-sick Japanese friend, Fuji, must get a letter to his best girl, back home in Japan. But, a secret mission to mail the letter from a Japanese-held island becomes complicated, when Fuji's letter gets mixed up in Binghamton's plan to distribute propaganda leaflets to the enemy.
Tinker is arrested for the theft of Binghamton's printing press, and The Captain taps Parker to be Tinker's Defense Counsel, in a trial which Binghamton, himself, will preside over. Parker and McHale must then stall the proceedings, while Gruber and The Crew execute a plan to get Tinker off the hook, with a bit of creative evidence-tampering.
A new Navy directive - Ordering all married Officers to be shipped home - Prompts Binghamton to scheme to get McHale married off to a shady saloon-keeper by the name of Kate O'Hara - An old friend of McHale's. But, neither Kate, nor McHale want to tie the knot, so they join forces, to try to thwart Binghamton's plan.
Gruber and the guys try to make some money with some phony pearl oysters, but their scheme backfires, when a greedy Binghamton takes over their operation. Then, when Chief Urulu muscles in on Binghamton's business, McHale and The Crew put a stop to the whole operation, by taking advantage of an old native superstition, and some Japanese technology.
Major complications develop when the guys send a chapter of Parker's war novel - Including a highly fictionalized account of his sinking of the biggest battleship in the Japanese fleet - To Parker's hometown girlfriend, in an attempt to help him win her heart.
Binghamton is offered a promotion and transfer up to Fleet HQ, but must first reconcile a shortage in the base's equipment inventory. After all is accounted for, except for one item - A barrage balloon - McHale and The Crew must race against time, in order to locate it, and bring it in, in time for Binghamton to be shipped out.
A business venture - Involving the manufacture and sale of sarongs to the Base personnel - Has the guys divided into two separate quarreling groups. When the feud escalates, Binghamton tries to take advantage of it's effect on them, during a PT Crew efficiency test - Their failure of which, would mean their being shipped out for re-assignment.
When Binghamton refuses permission for McHale and The Crew to put on a big show, to raise funds for the local Orphanage, Parker uses his newly-acquired skill as a Hypnotist, to make The Captain more agreeable. But the scheme is complicated by the visit of a Senator from the Armed Services Committee.
Parker - A dead-ringer for an important British General - Agrees to put his life on the line, by posing as The General, to divert the attention of spies, in New Caledonia, while the real General carries out a crucial invasion of a Japanese-held island.
Binghamton is ordered to purchase one of Chief Urulu's islands, for the construction of a radar station. But, Urulu - Knowing that he's got The Navy 'over a barrel' - Inflates the price of his real estate to ridiculous levels. So, McHale and The Crew try to help The Captain out, with a scheme to de-value The Chief's land.
Binghamton gets hold of Parker's diary, which includes details of the Crew's shady activities. After the guys steal the diary from The Captain's safe, Binghamton sets out to personally escort Parker to The Admiral. But, after falling into enemy hands, on the way, and being rescued by the 73 Crew, Binghamton changes his mind, after some gentle persuasion by McHale.
Five-time Oscar-winning Director John Burton comes to Taratupa, to shoot a documentary on PT boats, and their Crews, and McHale and the Crew successfully scheme to become the stars of the film. But, when they find out that Fuji has sneaked into the production, they must re-shoot the movie, themselves, with surprising results.
A Russian Naval Officer reports to McHale for PT Boat training, and, soon disgusted with the 73 Crew's lack of discipline, asks to be assigned to another Crew. But, when Binghamton finds out that the chosen Crew will shipped out to Russia, he talks the Russian into staying with McHale. McHale and the guys must then work up a plan to get out of the situation.
The French thief and con-artist first talks Binghamton out of a load of Navy supplies, then cons Parker into helping him get them to New Caledonia. McHale and the guys must then follow, rescue Parker, and recover the supplies.
After being restricted to base by Binghamton, McHale and the guys mock up a damaged PT boat, to look like the 73, so that they can sneak a load of building materials to a nearby island village, to help the natives rebuild, after an air raid. But complications develop, when Admiral Rogers visits Taratupa, to investigate.
While temporarily assigned to the 73 Crew, a lazy, pampered, rock and roll star is captured by a Japanese patrol, while out on maneuvers with McHale and The Crew, and holds a captive audience, making it easy for McHale and the guys to take prisoners.
To keep Parker from being shipped out, McHale and The Crew try to help the Ensign raise a thousand bucks, to replace a string of pearls - A gift for Binghamton's Wife - That were destroyed as Parker tried to save the Captain from what he thought was an air raid.
Impressed by a gangster movie he's recently seen, Chief Urulu plays mob chieftain and refuses to sign the document allowing The Navy the use of McHale's island. So, McHale and the Crew, and even Binghamton, Carpenter, and Admiral Rogers, join forces, and play their own mobster game, to try to make Urulu change his mind.
In temporary command of the base, while Binghamton recovers from a broken leg, and drunk with power, Carpenter gets the goods on The Crew, and has them up for Court Martial on several serious charges. McHale and Parker must then scheme to get Binghamton back in command, and The Boys off the hook.
Gruber and the guys pick up a few souvenirs, during a mission, unknowing that they're valuable items stolen by the Japanese, during the battle of Manila. When one of the items - A priceless antique tea set - Winds up as a wedding present for an Admiral's Daughter, McHale and The Crew must make a hasty trip to New Caledonia, where Parker must play the part of the officiating Chaplain, as part of a scheme to get it back.
Binghamton bows to pressure from the snobbish, swinging-bachelor Son of his former employer, in the hope of returning to his Stateside job, after the war. But, when the pressure becomes too great, The Captain conspires with McHale and the 73 Crew in a plan to get rid of him.
Christy has a chance to hear his little girl's first words, courtesy of a Ham Radio Operator, in The States, and, when Binghamton denies the use of the base radio, McHale and The Boys are forced to improvise, with a Japanese radio, captured during a raid on an enemy jamming station.