This episode reveals that, for years, Captain Reese has been plagued by memories of a series of racially-based murders which he has always been convinced were committed by Jordan Manning. In "Jane Doe", Manning is very much in the public eye as a reformed criminal who has published a book, Killing Mind. Reese is convinced that the book is more a secret confession than a novel. Indeed, he is sure that Manning has started killing again.
In his turn, Manning taunts Reese with his inability to catch him. As one of his first jibes, he sends Reese a bouquet of flowers. Superficially, it is very pretty: it includes pink daisies, baby's breath, and blue statice, which are used to set off several stalks of fluffy white flowers. Reese looks at them in disgust, and promptly tosses the bouquet in the nearest wastepaper basket. When Nick expresses surprise, he tells him that they were cotton blossoms.
The identity of the flowers is as obscure to many viewers as it is to Nick, for only people associated with cotton-growing are likely to be familiar with the appearance of cotton plants. However, Manning clearly expects Reese to know what cotton flowers look like, and to guess the significance of the gift. Slaves of African origin were the usual labour force on the cotton plantations of the southern US states in the years prior to the American Civil War. Since Reese is black, Manning intends the flowers to be interpreted as a racial slur.