The cartoon opens with titles featuring an instrumental of "The Sailor's Hornpipe" (also one of the theme songs to the Popeye cartoon series), seguéing to a scene of Sam digging a hole to bury his treasure on a beach. Sam is singing the stereotypical pirate shanty "Dead Man's Chest"—on the second strain, Sam switches from the typical "yo-ho-ho and a bottle of rum!" to a decidedly more original "yo-ho-ho and a bottle of... Ma's old fashioned ci-der" with a conga kick on the last syllable and a parody of "Dad's Old-Fashioned Root Beer", a well-known radio advertising jingle at that time.
In attempting to bury his treasure, Sam has encroached on Bugs' domain, as Bugs happens to have his rabbit hole there on the beach. When Bugs asks him who he is, he responds in his typical way: "What's up, doc?! I ain't no doc! I'm a pirate! Sea-Goin' Sam, the blood-thirstiest, shoot-'em-first-iest, doggone worst-iest buccaneer has ever sailed the Spanish main!"
To protect the location of his treasure, Sam prepares to shoot Bugs, claiming "Dead rabbits tell no tales!" Bugs then temporarily tricks Sam into trying to shoot himself in the head by saying: "Now, just a minute, Red. Ain't you got that wrong? You mean dead men tell no tales." After realizing he's been tricked, Sam grounds his teeth together so hard they shatter before he fires at Bugs.
Bugs escapes in a tied lifeboat, at one point rowing himself towards a ship without the boat. Following, Sam swims towards the ship to retrieve the paddles from where Bugs left them (oblivious that he doesn't even need them since he already made it to the ship without them), then returns to the lifeboat, which he then rows back to the ship.
As Sam searches for Bugs on the ship, he sees Bugs disguised as Captain Bligh (effecting the voice and thick-lipped appearance of Charles Laughton in his portrayal of Bligh in Mutiny On The Bounty). Sam takes criticism from "Captain Bligh" before being ordered a bunch of chores. Sam soon realizes he's been tricked (again), and follows a fleeing Bugs, but crashes into the mast while doing so.
In a side gag, Bugs is trying to hide and a pesky parrot keeps crowing to Sam, "He's in there! He's in there! Awk!" Finally, Bugs asks the parrot, "Polly want a cracker?" The parrot changes his tune, "Polly want a cracker! Polly want a cracker! Awk!" Bugs hands him a lit firecracker, which promptly explodes, blasting all of the parrot's feathers off, leaving him dazed and smoldering. His last words before he faints are, "Me and my big mouth!" For the next part, Bugs poses as the now-unconscious parrot to lead Sam into a cannon. Bugs lights the fuse, and then, KABOOM! The cannon explodes and Sam falls out of the barrel.
In a series of gags that mildly anticipate the Road Runner series, Bugs is in the crow's nest and Sam tries various unsuccessful attempts to get to him; for example, setting up a see-saw, standing on one end and tossing a cannonball on the other end, he springs straight up, crashes into the underside of the crow's nest, and falls back to the deck after his attempt to climb with trick rope given to him by Bugs failed as well. In another one, that skirts the laws of physics, Bugs tells Sam he's going to jump. Instead, Bugs drops a convenient anvil over the side of the crow's nest, Sam catches it, and the entire ship (except for the crow's nest) submerges. Sam mouths some apparent curses, then tosses the anvil over the railing and the ship resurfaces.
When Bugs comes down to check on Sam, Sam proceeds to attack him with his sword, making Bugs mad that he's "sore again". Bugs crawls in a hatch in the ship's side, with Sam following with his sword: "Ooooh, I'll keelhaul you for this!". When he opens the board, he is blasted by a cannon. Bugs opens the hatch to Sam's left and calls: "Yoo-hoo! Mr. Pirate!". Sam opens that board and, again, gets blasted by a cannon. Bugs opens another hatch and calls: "Oh, uh, Redbeard!". Sam, trying to avoid getting blasted again, decides to open up the hatch with his sword from a safe distance. Nothing there. Suddenly, another hatch opens in his face and a cannon blasts Sam once more, much to his annoyance.
Sam now chases Bugs again, and is now subjected to the famous lots-of-doors in-and-out routine (previously used in Little Red Riding Rabbit), which ends with Sam getting blasted by a cannon again. Sam confronts Bugs, who throws a match into the powder room, which a panicking Sam swiftly retrieves (a gag that would later be recycled into 1954's Captain Hareblower). This is repeated until finally, Sam is too late to retrieve the match that ends up exploding the pirate ship's powder magazine when he refused to go after another match again, reducing the ship to splinters. On his last nerve, Sam furiously chases Bugs with his gun: "Oooooh, I'll blast your head off for this!" until he seemingly has Bugs defeated ("Alright, now! I got ya cornered! Come out and meet your doom!") until a cannon blasts him once more. Finally, defeated, Sam raises the white flag. Bugs turns to the audience, puts on an old-style ship captain's hat, and paraphrases John Paul Jones, "I have not even begun to fight!"
Mel Blanc as Bugs Bunny, Yosemite Sam, and Parrot