Mattie and Grandfather have only been back at the coffeehouse for a few days when Mattie awakens to the voices of two men who have broken into the house. Mattie tries to stay quiet and hopes the men will not become aware of her since they believe the house is empty. When the men begin to play with Grandfather's sword near where Mattie is sleeping, she panics and tries to run out of the house. They grab her and try to force her to tell them where more valuables can be found. Amidst all the commotion, Grandfather awakens and comes downstairs. He attempts to defend Mattie, but is hit and beaten by the thieves as a result. Mattie grabs the sword and injures one of the thieves, which sends the two men fleeing.
However, once the thieves have left, Grandfather dies from his injuries, and Mattie is left all alone. She tends to the body, and the next day, she places it on the cart that comes around every day to collect the bodies of those who have died. However, Mattie is horrified when the cart arrives at its destination and she realizes that her grandfather is going to be buried in a mass grave without any sort of ritual or prayers. She demands that they say a prayer, and then she leaves them to bury her grandfather.
Mattie tries to go and buy food, but nothing is available at the market. She wonders how she will survive now that she is utterly alone. By chance, she sees that Andrew Brown is still operating his print shop, and she goes in, only to find that Mr. Brown cannot help her and is in despair himself. Mattie wanders the streets, wondering what she should do. She stumbles across a young toddler sitting in the street; she realizes that the girl's mother has died of the fever and she is now completely alone. Even though she has nothing, Mattie decides to care for the little girl, whom she names Nell. As Mattie and Nell move through the streets, Mattie catches sight of a woman who she thinks might be Eliza. Fortunately, Mattie is able to catch up with her and reunite with Eliza.
As they walk, Mattie explains to Eliza everything that has happened. Eliza tells her own side of the story: she nursed Mrs. Cook until she was recovered, and then Mrs. Cook went to the Ludington farm. Eliza stayed in Philadelphia to continue helping the poor and alleviating the suffering. As a member of the Free African Society, she has been actively working to help people impacted by yellow fever. She has assumed that Mattie and her family have been healthy and safe together this entire time. Mattie is eager to try to get to the farm to reunite with her mother, but Eliza urges her to wait and make a thoughtful plan. She takes Mattie and Nell back to the home she shares with her brother, Joseph. Joseph's wife has recently died, and he is struggling to care for their two young sons. The family also lives with an elderly woman named Mother Smith, who helps with housekeeping and caring for the children.
After everyone has eaten and the children have fallen asleep, Eliza speaks frankly with Mattie and tells her that she should take Nell to the orphan home. Mattie resists for a few days, during which time she helps Mother Smith with the house and caring for the children. She eventually concedes that she is only making it harder by delaying, and she takes Nell to the orphan home. However, the woman Mattie meets at the orphan home explains that they are barely able to care for the children they already have. Mattie decides it is better for Nell to stay with her, at least for the time being.
As Mattie, Eliza, and Nell walk home, they pass the Ogilvie mansion. Eliza explains that while Colette was sick with fever, she admitted that she was secretly married to her French tutor. This scandalized her mother and angered her sister, who had also been in love with the tutor. The whole family has fled from Philadelphia and is living together in very unhappy circumstances. When they pass the home of the painter, Mattie notices that flowers are being tossed out of an upper window; she realizes that Nathaniel is throwing her flowers.
Mattie and Nell are now accepted as a permanent part of Eliza and Joseph's household. Eliza invites Mattie to help her as she tends to the poor. Mattie is saddened and horrified by the suffering she sees all around her, but she enjoys feeling like she is helping others. One day, Mattie and Eliza come home and realize with horror that Nell and the two little boys have all fallen ill with fever. Eliza is frantic because the house is so hot and stifling, so Mattie suggests taking them all to the coffeehouse, which is airier and cooler.
At first, Mattie and Captain Cook have to cope with the challenges of finding food and water in the deserted city, with little infrastructure remaining. While these circumstances are very hard, they are not malicious. However, as this section of the novel reveals, when society starts to fall apart due to the epidemic, unscrupulous individuals can take advantage of these circumstances. It is clear that the coffeehouse has already been robbed when Mattie and her grandfather return, but they were not expecting the thieves to be bold enough to return. This shows that these individuals are systematically profiting from robbing abandoned homes and businesses and will return when they find a good target.
Mattie has shown bravery and resilience in a number of other circumstances, but in the confrontation with the thieves, she has to show a different type of bravery. She has to think quickly and abandon many of the ideas of being lady-like and polite. Once again, Mattie's unconventional upbringing becomes the key to her survival: if she had grown up like one of the Ogilvie sisters, she could never have fought off the thieves. However, Mattie's triumph is short-lived because of her grandfather's death. The death of Captain Cook is cruelly ironic because it seems more likely for him to have died from either yellow fever or something related to his advanced age. Instead, he dies as the victim of an act of selfish violence. While there are many tragedies throughout the novel, the Captain's death might be the most tragic because it arises out of human greed and malice.
The death of her grandfather takes Mattie to her lowest point. Up until this time, she has been driven to struggle and fight because people she cared about depended on her. It is telling that once she is utterly alone, Mattie begins to wonder if she would be better off simply giving up. Community and relationships are part of what have given her the will to try to survive. However, Mattie's crushing loneliness explains why she bonds so strongly with little Nell. With her grandfather dead and the fate of her mother unknown, Mattie is essentially an orphan herself. Taking responsibility for the little girl marks the completion of Mattie's growth to maturity. She steps in to a surrogate maternal role, and even though her own fate is so uncertain, she is prepared to do whatever she can to care for Nell.
Mattie opening her heart to Nell immediately brings her out of isolation and back into a community. Running into Eliza is a dramatic coincidence, but it symbolically reflects that, so long as Mattie keeps an open and caring heart, she will never be alone. Reuniting with Eliza gives Mattie the support and sense of family that she desperately needs at this time. More literally, Eliza gives Mattie and Nell a place to stay and takes her in as part of her own extended family. Eliza has been facing her own challenges, but as someone who is actively engaged in her community and has a strong commitment to helping others, she has also had a strong motivation to survive. Eventually, Mattie follows Eliza's mentorship to begin caring for the poor who desperately need help. While Mattie has never been rich, she has enjoyed some privilege and security, and seeing the dire circumstances of others helps her to realize that she can still be grateful.
Mattie also has to wrestle with questions of responsibility as she contemplates what is best for Nell. Mattie first makes the hard and selfless choice to take Nell to the orphanage, but she also discerns what is best for the young girl and acts accordingly. Earlier in the novel, Mattie failed to appreciate her mother wrestling with these choices on her behalf, but now that she is a caregiver, she knows what it means to try to make the best choice for someone else. Because Mattie and Eliza are caring for others and giving so generously of themselves, it is particularly cruel when the three children fall ill. All Mattie and Eliza have wanted is to keep the children safe, and once they realize that all of them have caught the fever, they spring tirelessly into action yet again.