Ali (Amit Sial) is a photographer and bike messenger who lives in New York. He develops a friendship and falls in love with a married woman, Saloni Oberoi (Mahima Chaudhry). When her husband, Harry Oberoi (Vikram Chatwal), is killed during the September 11 attacks, Harry's father, a retired Colonel (Anupam Kher), begins to take his aggressions out on Ali for being a Muslim. Although Mrs. Oberoi (Suhasini Mulay) tries to stop the Colonel's behavior, the situation escalates as the Colonel, himself, becomes the target of social post-9/11 aggression directed towards him because he is a Sikh.
The story revolves around a group of people who were not connected to each other in any way other than by ill fate. These were people from different parts of India who had traveled to the US and now were boarding the ill-fated flights that crashed into the Twin Towers and Pentagon on 9/11. The story tells us about the horror of the hijack and some of the incidents that occurred on board during those horrific minutes. Some of the characters in the film die in the accident.
First officer LeRoy Homer Jr. gets dressed in his F.A.A. official uniform, kisses his wife and leaves for work. The terrorist ringleader Ziad Jarrah shaves in his hotel room and then leaves for Newark International Airport.
The film tells the story of Nazneen, who grew up in rural Bangladesh, in the district of Mymensingh. At 17 she has an arranged marriage to Chanu Ahmed, who is twice her age. They soon move to Brick Lane in London, the centre of the British Bangladeshi community. She leaves behind her sister and her family home.
Two friends Derrick and Tico lost their jobs at a concession stand at the Statue of Liberty because of 9/11. In order to make money, they become drug dealers and participate in insurance scams. Derrick wants to go to college and has to support his two kids. When recruiters from the army come, Derrick decides to join the army because he is told that he'll get money for college and live rent free. When he tells his mom his decision, she says that she is afraid that he'll have to go to war. The recruiter tells him that his mom is only worried because it is her job as a mom.
Mustafa (Sayed Badreya) is a widowed Egyptian immigrant and the owner of Habibe's Café, a popular hangout in Los Angeles for those with Middle Eastern backgrounds. He is devoted to providing his son, Richard Chagoury, with a moral upbringing despite the pressures of contemporary American urban life. He also finds himself cast in the role of protector to his unwed sister Salwah (Sarah Shahi), for whom, by family and tribal custom, he is responsible for finding a traditional suitor. But his respect for tradition comes up against his own aspirations to adapt to the American Dream when he decides to open a new restaurant with a Jewish partner – his friend Sam (Tony Shalhoub). This unholy alliance is unpopular amongst the habitués of his café and the insular Arab community in which Mustafa resides. It is one of several personal points of tension that gradually build against the backdrop of larger, national events affecting the Arab-American community and lead to the explosive denouement of the story.
New York begins in the United States in 2008, with the arrest by the FBI of Omar Aijaz (Neil Nitin Mukesh) after guns were found in the trunk of a taxi cab he owned. Omar, a young Muslim man originally from Delhi, is then taken into custody and interrogated by FBI Agent Roshan (Irrfan Khan) (also a Muslim man originally from South Asia who has been living in the United States for twenty years). Omar then discovers that he was set up by the FBI in order to force him to spy on a former college friend, Samir Shaikh (John Abraham), whom he hasn't seen in seven years and who the FBI believes is a terrorist. In the process, Omar discovers that Sam has married Maya (Katrina Kaif) (a mutual friend whom Omar had a crush on in university) and finds out that Samir and Maya have a young son, Danyal (Aidan Wagner).
Montine McLeod (Melissa Leo) is a flight attendant who gets stuck with Omar Hassan (Anthony Keyvan) after their flight gets grounded in Longview, Texas, the morning of 11 September 2001. Omar is an unaccompanied minor; in the chaos that ensues, Montine becomes his temporary guardian. Montine later discovers that Omar's father works in the World Trade Center. She decides to drive the boy home after he informs her his father is at home waiting for him in New York. On the journey, they begin to bond and learn more about each other. Montine makes a stop on the way to New York as she receives a call that her mother is dying. Upon arriving at her mother's house, she finds her mother already dead. After dealing with her mother's death, she continues on the road to take Omar home. When they get there, they learn Omar's father has not been home in the two days since the destruction of the Twin Towers. Later that night, Montine receives a call from her employer and is forced to bring Omar with her. At the ensuing meeting, Montine is terminated; Omar is taken from her and given to his school head master for the night before leaving for a new school the following day (the reason he was on the original flight). The day Omar is set to leave for Los Angeles, he locks himself in the bathroom and refuses to come out. Montine is asked to come; she coaxes Omar out of the bathroom and she walks him to his flight to Los Angeles.
Yasmin is a young Muslim woman living in Britain. After Yasmin's husband is arrested on suspected terror charges following the September 11th attacks, she campaigns for his release from a holding center.
The film opens on the morning of September 11, 2001. United States Secretary of Defense Donald Rumsfeld is hosting a breakfast for a number of members of the United States Congress. The purpose of the breakfast was to procure an increase to the defense budget, with Rumsfeld claiming they will soon need the money as something big is likely to occur soon given the rise of Islamic Extremism against the United States.