There are a couple of storms in this novel, and one thing to ask yourself whenever there is a storm is "What is going on in the main character's mind?"  Storms (in TV, movies, books, etc.) usually are forecasting a character's internal conflicts.  The storm I think you're referring to is when Jim and Huck get separated.  Just before this, and after as well, Huck is torn between turning Jim in as a runaway slave and Miss Watson's property or helping him to escape because Jim is a good friend and a good man with a wife, children, feelings, and dreams for a future.

Another storm in the novel is when Jim, Huck, and the King and Duke are in the process of swindling the ladies out of their inheritance.  Of course, Huck is torn between helping the ladies (since they are nice and pretty, and treat him well) and helping the two imposters who threaten to be really bad news for Jim and Huck if they don't.