What are the orange pips and how are they used in the story? How does Holmes use them at the end of the story?
Literally, the orange pips are the seeds of an orange. But in terms of this story they are a warning sign. They are used by the Ku Klux Klan in this story as way to warn someone that the KKK is after them and will get them. If you have read "Treasure Island" this is similar to how the black spot was used in that book.
At the end of the story, Sherlock Holmes has figured out the identity of the KKK member who has caused the death of John Openshaw. He gets five pips out of an orange and sends them to that man as a way to scare him. But it is no use because the man's ship (he is a sea captain) is lost at sea and he never gets Holmes's letter.
In one of his strangest stories, "The Five Orange Pips" a mystery goes unsolved and the client of Sherlock Holmes dies before Holmes can divert the killer. The client is John Openshaw, the son of Joseph Openshaw and nephew of Elias Openshaw. John has come to Sherlock Holmes after the unsolved deaths of his uncle Elias, who had moved to Florida where he had a very lucrative plantation, and when the Civil War broke out, he joined the army and became a Colonel, and of his father in England.
The letters which have preceded the deaths of both men (in 1883 and 1884) have contained five oranges pips, or seeds, and have had the letters "K.K.K." stamped upon them. Now, John Openshaw has received a similar letter in 1885; this letter tells him to put the papers on the sundial. Of course, John has no idea what papers are alluded to; however, he assumes they are the papers that must have been burned long ago in his uncle's chambers, as he had smelled as seen paper ashes in the fireplace when he also witnesses a box of his uncle's which had K.K.K. He had retrieved a part of a sheet that was, perhaps, from a diary. It read as follows:
4th. Hudson came. Same old platform.
7th. Set the pips on McCauley, Paramore, and John Swain, of St. Augustine.
9th. McCauley cleared.
10th. John Swain cleared.
12th. Visited Paramore. All well.
Holmes promises to investigate and later determines from foreign postmarks and other information that the letters were sent from aboard a ship because the deaths occurred some time after the murders, so the mail ship must have arrived before the other ship. Holmes also looks up the Klu Klux Klan in his encyclopedia and finds this information:
Its outrages were usually preceded by a warning sent to the marked man in some fantastic but generally recognised shape—a sprig of oak-leaves in some parts, melon seeds or orange pips in others. On receiving this the victim might either openly abjure his former ways, or might fly from the country.
Unfortunately, John Openshaw is also killed. Then, before Sherlock Holmes, who has solved the mystery of the ships by researching in the Lloyd's Registry and before he can have the captain of the Lone Star to whom he has sent orange pips, James Calhoun, (former mayor of Atlanta when General Sherman invaded)arrested, the ship has sunk.