In the story, Bugs Bunny, asleep in a cotton field, is picked up by his cottony tail (which a worker mistakes for actual cotton) and bundled into a shipment put on a riverboat going down the Mississippi River (setting sail for Memphis, Vicksburg, Baton Rouge, New Orleans and Cuc-amonga). The cotton-picking scene is accompanied by presumably African-American voices singing "Dixie".
After seeing a steward forcibly eject a ticket-less passenger ("What? No ticket? We'll have no stowaways on this boat, sir!"), Bugs acquires some clothes and presents himself to the steward as a top-hatted gentleman. His self-assurance so clearly suggests that he belongs on the boat that the steward hesitates to even ask for a ticket, but rather than browbeat him with his presumed superior station, Bugs simply gives the man a ticket.
At this point Bugs could simply relax and enjoy the unexpected trip, which must eventually take the boat back to its starting point and allow him to disembark, but he prefers to seek an adversary with whom he can match wits. He finds one in the Yosemite Sam-esque Colonel Shuffle, a neurotic riverboat gambler played by Billy Bletcher. After Shuffle's gunplay clears out the customer base in the casino when another player tops his hand of three queens with one of four kings, Bugs remains as his only challenger in a poker game. Beginning with a hundred dollar stake (which amounts to only half a white chip), Bugs soon wins all of Shuffle's money including the original white half-chip when he tops the cheating Shuffle's hand of five aces with six aces. Literally beaten at his own game ("If'n I had four feet and went 'hee-haw', what would I be?", "Why, uh, you'd be a jackass"), Shuffle challenges Bugs to a pistol duel and an explosion from an exploding cigar, given to Shuffle by Bugs ("And the gentleman wins a cigar!"), leaves Shuffle in "blackface" and Bugs leads him in a dance to "De Camptown Races" (with Shuffle literally dancing off the boat, banjo in hand).
After Colonel Shuffle falls into the river and then comes back into the ship ("Why for did you splash me in the Mississippi mud?"), and a failed attempt to shoot Bugs with a waterlogged pistol (water flows out with a bullet sporting a sail), Bugs tricks Shuffle into buying a ticket to see "Uncle Tom's Cabinet" (word play referring to Uncle Tom's Cabin), only to fall back into Old Man River. Shuffle again tries to shoot Bugs ("Why did you dunk my poor old hide in Old Man River, when I bought a loge seat?"), only to be reminded, "Ah, ah, doc! It's full of water!" Shuffle points the pistol at himself, only to get blasted in the face, forcing him to temporarily hide in his hat. Angry, Shuffle chases Bugs down to the boiler room, only to end up in the boiler himself (causing the smoke from the smokestacks to warp into the word "YIPE!") and having no other option than to get change from Bugs for a cup to get water ("I seem to be in a terrible quandary, sir. Could you change a ten-spot, sir? I'd prefer a profusion of pennies"), only to shoot at Bugs again when he puts out his fire ("Thank you, sir. Keep the change.").
Bugs dons southern belle garb and appeals to another passenger to rescue "her" from Shuffle, whom the passenger throws overboard. However, after realizing that the "lady" he has assisted is a rabbit, the dumbfounded man has a nervous breakdown and steps overboard himself. Still in drag, Bugs notes: "Oh well, we almost had a romantic ending."
Mississippi Hare is available, uncensored, uncut, and the original end card restored, on Looney Tunes Golden Collection: Volume 4. On an audio commentary track, Eric Goldberg explains why the cartoon has been banned (though the racism in this cartoon, according to Goldberg, is "tastefully done" and not as blatant as in some other cartoons) and points out the presumably racist scenes (specifically the beginning with the cottonpickers, the Camptown Races scene, and the Uncle Tom's Cabinet gag) and the gun gag that was cut when it aired on ABC and the WB.