It is really difficult to say what the plot of this novel is since it consists of a number of vignettes that do not necessarily combine to make any sort of a sequential story.
However, I would say that the main plot has to do with Tom and Huck Finn and their interactions with Injun Joe. It follows the two boys as they see Injun Joe commit a murder. They then have to decide what to do about that seeing as how they fear that Injun Joe will kill them if they tell on him. Later on, they pursue some money that they believe that Injun Joe has hidden. At the end of the book, they find the money and are rich.
There are subplots within the book as well. You have Tom's "romance" with Becky Thatcher. You also have the whole subplot of Tom, Huck and their friend Joe running away to the island and having people think they are dead.
There are many little stories within this novel and they do not necessarily make one coherent plot.
There is no one single plot in the novel. As the title indicates, the book tells many stories covering some of the adventures Tom experiences as he interacts with the people and places around Saint Petersburg. Within each story, there are many of the same characters but with different degrees of involvement. The settings of the events change, from the picket fence around Aunt Polly's house to the schoolyard to the cave where the gang explored and discovered the hideout of Injun Joe. The conflict between Tom and Injun Joe comes the closest to an overall plot of any of the adventures in the story.