Before you start writing your plot summary, you should research James Joyce, so that you can describe when he wrote the story, how old he was when he wrote it, and its publication history (did it appear in a perioodical before being published in Dubliners?) Next, perhaps, note the ways in which it resembles his other work and any unusual characteristics.
For your actual plot summary, it is traditional to begin with a few sentences about each of the dramatis personae. You should cover the unnamed narrator, the boy's family, Old Cotter, Father Flynn, and Flynn's sisters.
Next, decide if you want to summarize events in actual chronological order or in the order in which we discover them as we read through the story. Much of the suspense of the story is derived information about Father Flynn only being revealed gradually.
Finally, you should draw your own conclusions about the character of Father Flynn and his influence on the boy.