U.S. Navy Ensign Frank Pulver feels unappreciated, as usual. Even when he personally aims a sharp object into the hindquarters of the hated Captain Morton, the happy crew cannot imagine that the all-talk, no-action Pulver could be behind it. A poll to guess at the identity of the "ass-sassin" results in votes for almost everyone except Pulver, which he bitterly resents. Shipmates like Billings, Insigna, Skouras and Dolan don't take Pulver seriously while despising the captain, who refuses to grant leave to a seaman named Bruno to attend his daughter's funeral back home. Doc is the only one aboard who believes in Pulver's potential at all. At sea for months at a time, Pulver is unable to indulge his greatest interest, women, until a company of nurses land on a nearby atoll. The head nurse is pleased to meet him when Pulver introduces himself as a doctor serving on a destroyer, but young nurse Scotty suspects the truth and a smitten Pulver confesses it to her, that he's no doctor and nothing more than a junior officer on "the worst ship in the Navy." Bruno becomes so deranged, he attempts to kill the captain. Pulver reluctantly intervenes, but the captain falls overboard, and is about to drown until Pulver lowers a life raft and dives in to save him. Separated from their ship, with the crew unaware for hours that they are missing, Pulver and Morton bicker aboard the raft. The ensign takes notes while the delusional captain reveals dark secrets about his past. In need of emergency surgery, Morton ends up owing his life yet again to Pulver, who follows Doc's instructions over a radio and removes the captain's appendix. Back aboard ship, Morton's natural tendencies resurface and he tries to return to his martinet ways. Although Pulver has the goods on him now he shows genuine compassion for the captain and convinces him to leave the ship for his own well-being. Morton takes his advice and departs, turning over command to the popular LaSeur.
Ensign Pulver began production under the working title "Mr. Pulver and the Captain". Location scenes for the film were shot in Mexico City and Acapulco, Mexico. Actor Jack Nicholson took it upon himself to assist director Josh Logan with casting, becoming an informal "assistant producer." Logan, who hoped that the film would repeat the success of Mister Roberts, recognized that it had fallen short of that mark, writing in his autobiography:
We thought we had everyone in the picture that anyone could ask for... But we had left out the most important thing: the catalytic agent, Mister Roberts. And without him, the story falls into shreds. No one really cares about the others enough to create suspense as to the outcome.
Concurrent with the release of the film, Dell Publishing issued a paperback novelization of the film by W. H. Manville, writing under the pseudonym he used for tie-in work, "Henry Williams."