The story is told out of chronological order, and this can make it difficult to put the pieces together as we read. In part 2, we learn that thirty years ago, Miss Emily Grierson "vanquished" town leaders, around the time that a terrible "smell" emanated from her property. The narrator also says that this was "two years after her father's death" and just a "short time after her sweetheart" had left her. At this time, even those few ladies who tried to visit Miss Emily were not allowed to enter her home.

We also learn, in part 2, that Emily's father felt that "none of the young men" who came to court her "were quite enough for Miss Emily." She had trouble parting with her father's body after he died, and people felt that "she would have to cling to that which had robbed her," in recognition of "all the young men her father had driven away." Essentially, Emily's father refused to allow her to marry anyone during his life, and then he left her all alone when he died.

In pat 3, we learn that Emily grew very sick after her father's death. When she recovered her health, she was often seen around town with Homer Barron, a Yankee laborer hired by the town to pave the sidewalks. People believed that "she was fallen," that she had slept with Homer. One day, she went to purchase arsenic, but she refused to tell the druggist what she intended to do with it.

In part 4, we learn that Homer went away, and people in town thought Emily would kill herself. The minister visited her about her relationship with Homer, and then his wife wrote to her relatives. Emily purchased some gifts that seemed to be wedding gifts for Homer: an engraved "man's toilet set in silver" and a full suit of men's clothes. Finally, her cousins appeared to have given up on her; they left town, and Homer returned. A neighbor saw Miss Emily's servant admit Homer to the house one night, and then no one ever saw him again after that. For a long time, no one saw Emily, and it was at this time that the men went to "sprinkle the lime" around her home to eliminate the bad smell. We also learn that her hair "attained an even pepper-and-salt iron-gray" color, a "vigorous iron-gray" that was pretty distinctive. After this point, Emily mostly remained a recluse. Time went on, and one day she died.

In part 5, the neighbors come to see the home after Emily's death, and Emily's servant simply leaves the house, never to return. Emily's family comes, and they bury her, but everyone "knew that there was one room" that "no one had seen in forty years." They waited until after Emily's funeral to force the door. The room was "decked and furnished as for a bridal," as though Emily had prepared the room for her wedding night with Homer, all those decades before. Everything is covered in dust, and the air smells "acrid," like a tomb. Homer's long-decayed body lies in the bed, "apparently once lain in the attitude of an embrace." On the pillow next to his, they find a "long strand of iron-gray hair," the hair that was so unmistakably Miss Emily's. She has, evidently, been sleeping next to his mouldering corpse for years.

Thus, we can now begin to put together the pieces: Emily, seeing that Homer would either choose to leave her or that she would be compelled to part with him, poisoned him with the arsenic. It was the smell of his decaying body that had so pervaded her property that men had come at night to deal with it decades before. Rather than be abandoned by Homer, as she'd been abandoned by other suitors and her father, she killed Homer to keep him with her. She seems to have indulged in some fantasy that they were married rather than come to terms with her terrible and unbearable solitude.

At the end of the story, the aged Emily dies. After the funeral, the townspeople break down the locked door to her bedroom. They find the room decorated as a bridal chamber, with the dead, decomposed body of Homer Barron lying on the bed. On the pillow next to where he is lying, as if in an embrace, they find the imprint of a head and a gray hair. This suggests that even at the end of her life, Emily was crawling into bed and sleeping in Homer's embrace.

Emily spends her life in stasis, living frozen in the past like her father before her. She has never accepted reality, such as the need to pay property taxes. When she can't have Homer, who must have told her he was leaving, she poisons him with arsenic so that she can freeze time and have him with her forever.

This is Faulkner's way of condemning the South for trying to freeze time and live in the past, as if they never lost the Civil War and as if their old way of life had not changed. Living in this kind of stasis is like living with a corpse, Faulkner implies: it is not sweet or nostalgic but a grotesque form of collective mental illness.

At the end of the short story, the townspeople attend Miss Emily Grierson's funeral, and several curious citizens enter her home in order to clean out her possessions. The townspeople are curious to enter Emily's upstairs room, which nobody has been seen in over forty years. They break down the upstairs door to discover a room that is "furnished as for a bridal," and everything is covered with a thin layer of dust. They then discover Homer Barron's skeleton lying on the bed next to a pillow, along with a strand of iron-gray hair on it. The citizens' dramatic discovery suggests that Emily Grierson has been lying next to her dead lover's corpse each night, which is both shocking and macabre. The mystery of Homer Barron's disappearance is solved, and Emily Grierson's mental instability is portrayed by her implied necrophilia.

At the end of the story, the narrator is describing the state of Miss Emily's house after her death.  The townspeople, particularly townswomen, have gone in to clean out the house in the wake of Emily's passing.  This is the first time in years that anyone has been inside the house, with the exception of Miss Emily's servant. 

When the women go into Miss Emily's bedroom, they find the skeleton of a man that has been long dead.  They also find the toiletry kit of the man that has been etched with the initials "HB".  This confirms that the dead body is that of Homer Barron, Miss Emily's beau from long ago.  The townspeople had believed that Homer had left Miss Emily because he suddenly stopped being seen.  They had even believed that Emily was going to commit suicide, because she had purchased arsenic at the time of his disappearance.  However, this body tells us that Emily had used the arsenic on Homer, killing him and keeping his body in the house - which explains the smell from the house that the townspeople had been concerned about years before. 

Beside Homer on the bed is a strand of iron-gray hair - Miss Emily's hair.  She was so attached to Homer that not only did she kill him to prevent him from leaving, but she also lay in a bed with his dead body.

Creepy, huh?