He first appears to the reader as a strict, bitter man who finds fault with everything and is never satisfied. However, he quickly reveals that not all is well aboard the ship, and his first conversation with Jim Hawkins, Dr. Livesey, and Squire Trelawney foreshadows the eventual mutiny of many of the Hispaniola's members under the leadership of Long John Silver, a cunning and wealthy one-legged pirate. When the Hispaniola finally reaches its destination and the pirates rebel, he organizes the faithful crew's flight from the Hispaniola onto the shores of Treasure Island, and helps in gaining a stockade on the island. The first thing he does there, after the initial setup, he hoists the Colours over the structure refusing to remove it when the mutineers use the Flag is the mark for their cannonade. The next day, he attempts to hold a parley with 'Captain' Long John Silver, but the negotiations fail due to the arrogance of Silver in his apparent tactical superiority and the stubbornness of Smollett in his refusal to negotiate with good-for-nothing scoundrells. (Indeed, Smollett admits that he has goaded Silver on purpose, reasoning that battle is probably inevitable and might as well be fought sooner rather than later, while they are alert and fresh.) As a result, Silver storms off in a rage, and Smollett is left to organize the defence of the stockade. In the subsequent battle he is wounded by two bullets, though his life is never in danger, and disappears from the story for the most part. In the end, he and the faithful crew sail back to Bristol laden with treasure. He retires afterwards from sea life, secure financially and exhausted by the affair.
Captain Smollett's role in the story is crucial, but he is usually remembered for his militaristic tough-but-fair personality. He is obsessed, as might be expected from any naval captain, with duty and expects all his orders to be followed to the letter. On the second day of the stocade defence he does not hesitate to admonish the crew, including his superiors, the Doctor and Squire Trelawney, for abandoning their stations to watch his negotiations with Silver. Yet he fairly praises Abraham Gray, a mutineer who defects to their side, for staying at his post dutifully.