As Mattie and Grandfather journey out of the city, they notice that many others are also fleeing. After they have been traveling for a few hours, their wagon is stopped by a group of soldiers. Before they can pass through the town they are approaching, they will need to be examined by a doctor and confirmed to be healthy. Grandfather begins coughing, and the doctor orders him to return to the city. Before Mattie and Grandfather can do anything, the farmer driving the cart throws them off and drives off without them. Mattie and Grandfather are now stranded on the roadside. They try to start walking, but Grandfather is too sick to go far. Mattie leaves him resting and goes to get water. Mattie is also able to find some food, and they sleep for the night. The next morning, Mattie is growing increasingly worried about what will happen to them. After desperately trying to find more food, Mattie approaches a nearby farmhouse to ask for help. The farmer drives her off because he fears she might carry fever. After wandering about in search of food, Mattie collapses.
When Mattie wakes up, she is in a hospital and knows that she is suffering from yellow fever. She wakens again a few days later and learns that she is being nursed by a woman named Mrs. Flagg. Grandfather brought her to the hospital at Bush Hill (formerly a mansion) after she collapsed, and she is now on her way to recovering. Grandfather also explains that after he got Mattie to the hospital, he went back to the coffeehouse to see her mother. However, no one was there, so Grandfather assumes that Mrs. Cook has also recovered and gone to the Ludington farm to reunite with them. He has sent her a letter to explain everything that has happened. Mattie spends another ten days in the hospital recovering, and she hears horrifying stories of how the epidemic is raging everywhere and more and more people are falling ill and dying. She is eventually moved out of the main hospital into a barn where patients close to recovering are kept. As time passes, Mattie becomes more and more anxious about why her mother has not responded to letters and why no one can track her down.
When Mattie has fully recovered, the administrator at the hospital claims that she will have to go to the orphan house since her mother cannot be found. Fortunately, Grandfather explains that he will care for Mattie, and the two of them leave the hospital to return to the city. On the way there, they travel with a woman named Mrs. Bowles, who suggests that Mattie find a way to help those who are suffering. She also advises Mattie and Grandfather to be very cautious, as the city has become a dangerous place. Grandfather explains that they hope to head to the Ludington farm, but they learn that letters are no longer being delivered, so they have no way to make plans. Mattie is horrified as she realizes that the city is deserted and that people are literally being left to die in the streets. Worse, when they arrive at the coffeehouse, someone has broken in, ransacked the place, and stolen all of the food.
Although Mattie feels overwhelmed, she takes charge of the situation since her grandfather's health is fragile. She works very hard to start to fix up the house and find some food for them. They agree they will try to survive and stay at the coffeehouse as long as possible, hoping that Mattie's mother will eventually contact them there.
Epidemics at different points in history have often motivated individuals to try to flee to more rural areas, believing they would be safer there. However, individuals moving from locations with high incidents of disease to areas where infection rates are lower runs the risk of simply increasing infection rates and spreading disease to a wider geographic area. The fear and suspicion that arise as Mattie and Captain Cook try to flee the city show how the epidemic can bring out the worst in people. The soldiers and the farmer driving the wagon cannot bother to be compassionate to a young girl and an elderly man because they are preoccupied with their own fears. While Mattie and Captain Cook believed they would find safety by getting out of the city, they end up in an even more dangerous position because they are stranded far from help, with little access to food and water. In these isolated areas, being able to depend on others would usually be very important; when Mattie tries to seek help, she is driven away due to fears of contagion.
Mattie moves further into a position of adulthood as she takes responsibility for finding food, water, and shelter for herself and her grandfather. Mattie has lived mainly in an urban area, but she is clever and resilient. She is able to locate a water source and even devise a method for attempting to catch fish, showing that Mattie is able to adapt to new and challenging circumstances. However, Mattie abruptly falls ill, likely because she contracted the fever while caring for her mother. During these types of disease outbreaks, when many people would be cared for at home by family members, this type of tragic transmission would be very common. Once she falls ill, Mattie is now the one who is totally vulnerable. Fortunately, her grandfather rises to the occasion, and this shows the strength of family bonds. Captain Cook has been ill himself, but in a moment of crisis, he is still able to find the strength to get help and get medical care for his granddaughter.
Possibly because she is young and strong, Mattie is able to make a good recovery. Once her health is on the mend, Mattie's most pressing problem is the confusing separation from her mother. At a time when the city was in chaos and communication was limited, this type of disorientation could happen surprisingly easily. Neither Mattie nor Captain Cook can figure out where Mrs. Cook is, and they have to tolerate uncertainty amidst an increasingly chaotic atmosphere. The conversation between Mrs. Bowles and Mattie shows another woman stepping into a maternal role in the absence of Mattie's mother. At this point, Mattie is preoccupied with taking care of herself and her family, but Mrs. Bowles points out that Mattie is now actually in a privileged position. With immunity from the fever, she can help others, and in that way, her own suffering with the illness will not be meaningless. Even though it is a small interaction, this conversation shapes Mattie's priorities and pushes her further towards becoming a caring, responsible, and unselfish young woman.
In the short term, however, Mattie has many challenges to confront when she and her grandfather return to Philadelphia. Albeit in different ways, the situation in the city is almost as precarious and dangerous as the situation when they were stranded in the countryside. Urban environments tend to be dependent on systems of commerce and supply to provide food and other necessary items, and once those systems break down, it can be very hard to get what one needs. Mattie once complained about doing basic chores at the coffeehouse, but she now has to take on responsibility and hard work to keep herself and her grandfather alive. Although she is afraid and nervous, Mattie further demonstrates her maturity by showing courage and optimism to her grandfather.