Ground Zero is told in alternating chapters that follow Brandon's storyline (set on September 11, 2001) and Reshmina's storyline (set on September 11, 2019).
The novel opens with nine-year-old Brandon accompanying his father, Leo Chavez, to the World Trade Center. Leo works as a kitchen manager at Windows on the World, a restaurant situated at the top of the North Tower, on floors 106 and 107. Brandon has been suspended from school following a physical altercation between him and another boy. While heading in to work, Leo advises his son that he should work to resolve his issues, as fights and revenge lead only to more trouble.
Once in the restaurant, a fire erupts in the kitchen, distracting Leo. Brandon sneaks out to purchase a new pair of Wolverine gloves from the Sam Goody store in the mall underneath the Twin Towers; he wants to replace the pair he broke, as they belonged to his friend. Brandon is in the elevator when the first hijacked plane hits the North Tower. The elevator stops moving, and Brandon breaks free with the help of his fellow passengers, who he then helps rescue with the aid of office workers on the 85th floor. Rather than go down the emergency stairs with the group, Brandon climbs up, hoping to reach his father on the top floor. However, he encounters debris that blocks his way up. When Brandon realizes the wall of the building is open to the air, he crawls along a ledge, eventually being pulled inside by Richard, a businessman.
Brandon and Richard check up on other survivors as information about what happened trickles in. When Brandon learns a plane hit the building, he is more eager to get to his father; however, the plane has taken out the 98th to 94th floors, meaning he is cut off from his father on 107. People have been advised by the authorities to stay where they are and wait for rescuers. Brandon is on the phone with his father when a second plane hits the South Tower; Leo realizes they are under attack. Brandon slowly makes his way down the stairs with Richard and other office workers. By the time they reach the ground level, they are told to go through the underground mall; Brandon sees that the police are blocking evacuees' views of the bodies and bits of the plane falling on the plaza. The South Tower collapses when Richard and Brandon are in the underground mall. Brandon finds Richard and other survivors in the dark, then leads them out to street level. Brandon is there just in time to see the North Tower collapse and kill his father. The storyline ends with Brandon going home with Richard in Queens, where he will begin living with Richard's family.
Reshmina's storyline is set in the mountains of northeastern Afghanistan in 2019. At twelve, she practices her English despite her mother's wish that she focus on chores and housework, which her mother believes are the most important things for a woman to know. Reshmina worries her twin brother, Pasoon, will inevitably join the Taliban soon, because he already looks up to older boys who have joined rather than toil as goat herders. One day, Afghan National Army and American soldiers arrive to search the homes of villagers, including Reshmina's family, because they've heard a tip that the Taliban is storing weapons in the village. She has never seen Americans in her community before, even though the US has been in the country since 2001. She learns from her brother that the Taliban planted the rumor in order to ambush the ANA and Americans; Reshmina learns this too late to stop the bloodshed.
After the firing ceases, Reshmina goes out to collect firewood. She encounters Taz, an American soldier who has been wounded and temporarily blinded. She wants to ignore him and let him die, but his request for help reminds her of her people's code of honor, which says an Afghan must help anyone—even an enemy—if asked. Reshmina leads the blinded soldier to her home. Her father agrees to give him refuge, despite the personal risk to the family and their neighbors. While Reshmina's father walks a long distance to inform the ANA so Taz can be evacuated, Pasoon runs to tell the Taliban. Reshmina follows Pasoon into the hills in the hopes of getting him to change his mind about betraying the family, as he ought to know that the Taliban will kill their family and other villagers as punishment for harboring the American. However, her attempts are in vain, and Pasoon alerts the Taliban.
Reshmina runs back to the village to warn her family and neighbors about the Taliban's impending assault. She is just in time to get Taz, her family, and other villagers into the old tunnels beneath the hillside village. Meanwhile, Americans and Taliban exchange fire. Explosions rock the ground and bury some villagers in rubble. Reshmina discovers a room full of antiquities and weapons from the many foreign nations that have tried to impose their will on Afghans over the centuries. She thinks of it as a "shrine to failed conquerors." Reshmina escapes the room by detonating an old Soviet landmine.
Reshmina wakes up down by the river, and learns her family members and Taz have survived. Taz says that he got into the military at eighteen because he wanted to bring the people who did 9/11 to justice. It is at this point that Taz reveals his real name—Brandon Chavez—and the reader realizes Brandon has been a part of both storylines. Taz is surprised when Reshmina and her family haven't heard of 9/11 or the Twin Towers. He sheepishly explains that Afghans weren't responsible for the attacks, but the Taliban refused to hand over Osama bin Laden to the Americans, which led to the 2001 invasion and toppling of the Taliban regime. The Americans continue shooting missiles at Reshmina's village—ostensibly to target Taliban members—and she sees her family home get destroyed.
When Americans arrive with survival supplies and promises to compensate locals for the damage, Reshmina erupts in anger and despair at Taz, blaming him and other Americans for doing more harm than good in her country. Taz admits that, while he got into the army for a good reason, he no longer knows why they are in her country. He says it's bad if the Americans stay, and bad if they leave, because the Taliban will regain power. Reshmina suggests that Afghans need an opportunity to work things out for themselves, without the involvement of richer, more powerful countries. Before leaving, Taz gives Reshmina the Tasmanian Devil toy that he keeps strapped to his uniform as a talisman of good luck; it was with him when he led Richard and the others out of the underground mall beneath the Twin Towers. Reshmina's storyline ends with her recognizing Pasoon's figure in the distance. He waves to her, but she leads her father away from him, telling her father, "I've found another path."
