Dr. Kenn becomes more and more frustrated at the unwillingness of the women of St. Ogg's to employ Maggie. He decides to offer her a job as governess for his children. The town soon begins to talk of Maggie's power over Dr. Kenn and the horrid possibility of their marrying. The Miss Guests report the connection between Maggie and Dr. Kenn in a letter to Stephen. They also ask Stephen to join them on the coast, where they will be taking Lucy to rest.
Lucy has been gradually recovering. Maggie longs to see her but knows it would cause Lucy too much agitation, even if she were allowed. Maggie despairs upon hearing that Lucy will soon leave for the coast.
One evening, Maggie hears someone come in the house. She feels a hand on her shoulder and hears Lucy's voice call her name. Lucy has snuck away from her home to see Maggie and forgive her. Maggie repents and explains that she never meant to deceive Lucy. Lucy comforts Maggie, acknowledging that they have all suffered. Maggie asks Lucy to forgive Stephen as well, but Lucy trembles and is silent. Lucy's maid, Alice, interrupts, to urge Lucy to hurry. Lucy hugs Maggie and tells Maggie, "you are better than I am," before leaving.
The day after Lucy's visit the weather changed in St. Ogg's and rain has fallen continuously, making the Floss dangerous, especially for nearby houses such as the Jakins'.
It is September, and Maggie sits, the last one still awake in the house, with a letter from Stephen in front of her. Two days prior, Dr. Kenn, finally overcome by the slanderous gossip about him and Maggie, asked Maggie to leave St. Ogg's for a while. Maggie trembles at the thought of the loneliness she will face, having left St. Ogg's.
Stephen's letter reports that he is back from Holland and is in Mudport, unbeknownst to anyone else. He reproaches her for her cruelty to him. He stresses the severity of his suffering since their parting and begs her to ask him to come to her. Maggie is tempted to accept this escape from her loneliness and exile. But soon she remembers her feelings upon having read Philip's letter and upon having met with Lucy and begins to pray. She cries out for Stephen to forgive her, saying of his suffering, "It will pass away. You will come back to her." She then burns the letter and resolves to write him a letter of final parting tomorrow.
Maggie resolves to herself, "I will bear it, and bear it till death But how long it will be before death comes!" Maggie falls on her knees and suddenly feels cold river water flowing under her. The Floss has begun to flood. Maggie wakes up Bob and his wife. The first floor is being inundated, and Maggie wades through the water to get Bob's two boats outside of the house. She gets one of the boats to Bob, before she and the other boat are carried out onto the open water. Maggie begins to paddle towards the mill in the dangerous current of the Floss. Maggie rides the current downriver, then paddles the boat out of the current and over toward the Mill in a feat of strength. Maggie reaches the mill. Tom is at the attic window. Mrs. Tulliver had gone to the Pullets' the previous day. Tom gets in the boat and takes the oars. When they reach the current again, he finally realizes what a miraculous effort Maggie has made to save him. He speaks only his name for her, "Magsie!" They row on towards the Deanes' and Lucy, but before they can get there a piece of wooden machinery capsizes their boat, and they drown together embracing each other.
It is five years later, and all of the characters of the novel are still living except Tom and Maggie. Philip and Stephen visit Maggie's grave. Years later than this, Stephen and Lucy visit Maggie's grave together, and Philip visits alone. Maggie and Tom's tomb reads, "In their death they were not divided."
In the final chapters of the novel, Lucy's visit, along with Philip and Stephen's letters, provide a somewhat constructed means by which Maggie has interviews with all of the characters close to her and is forgiven before her death (which they could not have predicted). Yet the total effect of these final interviews is not one of tranquility. Philip's and Lucy's words bring Maggie happiness and also added grief over the inherent goodness of the very people she has betrayed. Stephen's letter arrives as another trial. Even after her reconciliation with Lucy and Philip, Maggie feels the temptation of the life that Stephen offers. The effect of the letter on her is shown in the face that she "hears" the letter rather than reads it, much in the same way she heard a voice speaking the text of Thomas a Kempis rather than reading it silently.
The ending scenes, and especially the flood, of The Mill on the Floss have been criticized for their unrealistic quality. Maggie's plea to know how much longer her painful life will last is met almost supernaturally by the immediate onset of the flood. Yet we know that George Eliot had planned on the flood from the beginning and meant for it to seem a realistic occurrence. Her first work on the novel consisted of research in London into the Annual Register for cases of flooding from earlier in the century. The flood, like Wakem's purchase of the mill, provides a tragic circumstance in which the tragedy of Maggie's character becomes clear. The flood also provides the heightened atmosphere of danger and sense of the power of Nature that is needed to properly put Maggie and Tom's differences into perspective. Maggie's heroic feat of strength and selflessness in her rescue of Tom reveals her true character to the stubborn, narrow-minded Tom. Tom has been insisting through the novel that Maggie recognize his right to care for her and dictate her actions, but in the end, it is Maggie who cares for both of them and shows herself capable. The depiction of Maggie's rescue of Tom recalls the story of St. Ogg's and evokes the trait of sympathy that lies at the heart of the St. Ogg parable. Maggie's extreme capacity of feeling for the plight of others is what overcomes Tom's bitter sense of justice and reunites them. The end of The Mill on the Floss signifies a return to the beginning of the novel, to Maggie's nostalgia for their childhood days when she and Tom were united. In the boat, Tom calls Maggie by her childhood name, "Magsie." They are drowned in each other's arms, and the final imagery of the scene directly evokes their childhood and reinterprets that time as idyllic, saying, "brother and sister had gone down in an embrace never to be parted: living through again in one supreme moment the days when they had clasped their little hands in love, and roamed the daisy fields together." This dramatized return to beginnings affirms Maggie's impulses to abandon Stephen and return to her origins, vindicating her at the same moment that she becomes a tragic hero.
The postscript "Conclusion" serves to place Maggie (and Tom) in the larger context of their landscape and society. The same flood that took their lives has left its mark on the countryside, implying that Maggie and Tom's deaths left a mark on the community. The "Conclusion" also assures us that Stephen and Lucy have begun a new relationship and that Philip remains faithful to Maggie's memory through a lifetime.