Abdulrahman Zeitoun, owner of a painting contractor business, lives in New Orleans, Louisiana with his wife Kathy and their four children. Friday, August 25, 2005, is a normal day for the family: the children attend school, Kathy fields phone calls from clients and Zeitoun visits his many work sites throughout the city to liaise and oversee. Early reports of a tropical storm heading towards the Gulf is, initially, not a concern.
Through a series of flashbacks, we learn about Zeitoun’s past. He was born in Jableh, Syria and worked as a sailor for many years before settling down in New Orleans. When he was ready to marry, his was introduced to Kathy, a native of Baton Rouge and converted Muslim, through mutual friends in the Islamic community. In addition to a son from a previous marriage, Kathy and Zeitoun are raising three girls. Zeitoun is revered in his adopted city as a fair and hardworking businessman. Despite facing some mild prejudice after 9/11, Zeitoun has built a life that is both financially and socially successful. He is known simply as "Zeitoun" to his many neighbors, friends and loyal clients.
As reports of Katrina's growing strength amplify, Kathy is unnerved by a story of a family lost at sea during the storm. She urges her husband to evacuate. Zeitoun agrees that she and the children should go to her family's home in Baton Rouge, but he won't be dissuaded from his plan to stay in town to keep an eye on their home and work sites. Katrina is upgraded to a hurricane, yet Zeitoun is still not worried. As the rains come, Zeitoun manages to keep on top of the minimal damage while reminiscing about his idyllic childhood in Syria.
But Hurricane Katrina becomes one of the most catastrophic storms in American history, and Zeitoun realizes that the damage to his own home and city will be extensive. Zeitoun prepares his house for flooding but it not prepared for what he finds outside. He discovers that his entire neighborhood is under nine feet of water. He realizes that the levees surrounding New Orleans must have broken - the clear, clean water is from the sea. Zeitoun travels around the neighborhood in an old canoe, helping elderly people who are trapped in their homes escape. He must do this with the aid of other civilians, since he finds the police and National Guard inefficient and unwilling to help.
From Baton Rouge, Kathy hears that the National Guard and other military have been sent to New Orleans to maintain order. The rumors of violence and lawlessness make Kathy frantic. Able to contact Zeitoun at first on his cell and then on a landline in one of their properties, she begs him to leave. But Zeitoun believes he is on a mission from God, tasked with helping people and pets left behind in the devastation. Meanwhile, Kathy deals with growing tension with her family in Baton Rouge, who disapprove of her hijab and her refusal to eat pork. Realizing that New Orleans will be uninhabitable for weeks, she decides to move the kids to her friend Yuko's home in Phoenix, Arizona. She and Zeitoun maintain daily phone call updates, which keep Kathy's fear at bay.
In New Orleans, Zeitoun encounters tenant Todd Gambino and friend Nasser Dayoob, who also chose to stay in the city. They work together to rescue people, but the city is becoming increasingly dangerous and polluted. When the men finally decide to leave when mandatory evacuation is declared, they find out that the rescue helicopter has crashed. They are stranded. Later, they meet Ronnie, a young man squatting Zeitoun's rental property where Todd lives. Since the building is relatively undamaged, the phone still works and Ronnie seems to be no threat, Zeitoun allows him to stay. When showering, a group of armed men burst through the door.
Zeitoun does not call on Wednesday as promised. Kathy becomes very anxious, especially when Zeitoun does not call for another two weeks. She and Zeitoun’s brother, Ahmad, try to find Zeitoun to no avail. Eventually, she begins to believe that Zeitoun is dead, and starts to plan how to raise her children without him. Finally, she receives a call - not from Zeitoun, but by an anonymous missionary who informs her that her husband is being detained at Hunt Correctional Facility in Louisiana.
The narrative doubles back to Zeitoun’s shower at the rental property. As he steps out, a group of armed law enforcement agents burst in, arresting Zeitoun, Nasser, Todd, and Ronnie. They are taken to a makeshift prison located in a bus station, where they are subjected to strip searches and interrogation without being read their rights or charged of a crime. They are held in a crowded, miserable outdoor prison, where they are subjected to brutality by the guards. To make matters worse, Muslims Zeitoun and Nasser cannot eat most of the food they are given, as it includes pork.
Eventually, the men are transferred to Hunt Correctional Facility - still without being properly charged. Although the conditions here are marginally better, Zeitoun is still not allowed to call Kathy, and he begins to despair that he will ever be released. Zeitoun suffers undiagnosed pain and loses weight rapidly. He believes that hubris and pride are responsible; by not heeding Kathy's warnings, he has placed himself in this predicament. He appeals to a sympathetic missionary to call Kathy on his behalf, and he reluctantly agrees although it is against the rules. The next day, Zeitoun is interviewed by the Department of Homeland Security. Their agents are relatively friendly and also agree to call Kathy.
After learning Zeitoun’s location, Kathy is able to post bail using their office building as collateral. Soon after, the charges against him are dropped. After his release, the family sets about gutting and rebuilding their home in New Orleans. They continue to have problems with the bureaucracy of FEMA and the legal system. FEMA offers them a free trailer to live in but does not give them a key, and then refuses to take it away from the Zeitouns’ property when it is no longer necessary. They file a lawsuit demanding compensation for Zeitoun’s incarceration, but it had not progressed much by 2008, when Zeitoun was written.
Both Zeitoun and Kathy continue to suffer symptoms of post-traumatic stress, but they persevere and refuse to leave New Orleans. Zeitoun takes great satisfaction from rebuilding both the city (through his contracting business) and his life (through his family).