The movie starts off in San Francisco of November 2007.
Rizwan Khan (Shahrukh Khan) is jotting down notes (President Bush's itinerary) from a computer. We then see him arriving at an airport with a back pack. He buys a ticket and gets in line for a security check. The guards ask the people in line to open their bags and laptops, etc for convenience. Rizwan is fumbling with pebbles in his hand and starts reciting a Surah in Arabic (a verse from Holy Koran). A lady in front of him stares at him suspiciously. Next he is being asked by an officer to come with him. We see him in a room with couple of officers. They are doing a full body search and he is stripped down to just his undershirt and boxers. The officers find an Autism awareness ID card with Rizwan's name and his picture. The officers tell him that his name did not raise red flags in the system, so he is free to go. While gathering his things together, he mumbles about missing his flight and that he has no more money to buy a plane ticket and he has to make his journey to meet the President by bus now. The officer asks him why he wants to meet the President. He says he wants to tell the President of United States that his name is Rizwan Khan and he is not a terrorist. This remark makes the guard tease him. The officer says that when he meets the President, tell him that he says "howdy". Rizwan writes the name of the guard and his message "howdy" in his journal.
Rizwan then goes out and sits on a bench and starts writing to/for Mandira. He says that he is better at writing his feeling for her than at expressing them. He loves her and is in pain because of their separation. Rizwan says that he was born in India and no one knew what was wrong with him. We see flashback of his life in India. His father used to leave him in a junkyard while he worked as a mechanic in an auto workshop. Rizwan learned to fix things while spending time at the junkyard by him self. His father dies. His mother is very loving and patient with Rizwan. He has a younger brother Zakir. One day Rizwan gets beaten up at school. His mother then takes him to a very educated man and asks him to take Rizwan under his wing and teach him everything. We see that their mother is more devoted to Rizwan and Zakir always comes second in her life. Rizwan says that as soon as Zakir turned 19 he left for America. Both Rizwan and his mother missed Zakir but Rizwan got used to his absence after a while. We see a phone conversation between Zakir and his mother. He tells her he is getting married and that he has filed papers so his mother and Rizwan can come live with him in America. His mother is sad at not meeting her daughter in law. Rizwan tries to console her by giving her timed hug. He does not like to give hugs but only do so because of his mother, who loves to hug him. He then tells the viewers that his mother is died soon after and we see an airplane taking off. Next we see a cab stopping in front of a house in San Francisco. Rizwan and Zakir get off the cab. A woman in a scarf comes running down the stairs to meet them. Zakir introduces her as his wife Hasina. Rizwan acts aloof and tries not to meet her eyes. Hasina finds this strange. She notices his odd behavior, his intense dislike to yellow color, loud noises etc. She then takes him to get evaluated. They find out that he suffers from Asperger's syndrome. Hasina gives Rizwan a camcorder and tells him to record things that way it will be easier for him to get used to new things and places.
Zakir is a supplier for Herbal Beauty products. Rizwan becomes a door-to-door salesperson for those products. He then meets Mandira, who works at a Salon. She is divorced with a young son and dreams of owning her own Salon. We see Rizwan spending time with Mandira and then proposing. Meanwhile she and her son have bought a house and move to California. Mandira declines first and later accepts the marriage proposal. Zakir opposes this marriage on the basis that Mandira is not a Muslim. He then tells Rizwan that if he gets married to her he will not be welcome in his home. We see Rizwan traveling in a bus. The story goes back and forth and I kind a lost track of the order.
We see Mandira and Rizwan getting married amidst her friends. Their neighbor Sarah comes over with her family. Her son Reece is the same age as Mandira’s son Sam. We see them at a Salon opening. The Salon belongs to Mandira. We see that Mandira and Rizwan leading a very happy life with each of them following their respective religion. Then 9/11 happens. Things change for everyone. Mandira loses her Salon and finds a job working at another Salon. Zakir asks Hasina to stop wearing her scarf when she gets attacked. Mandira comes and visits them after the incident and Rizwan and Zakir make peace. Sarah’s husband gets killed covering the Iraq war. At his funeral Reece’s blames Sam for his father’s death. Sam tries to reason with him but to no avail.
Sam gets into a racial provoked fight at school and dies. Mandira blames Rizwan for his death saying He died because his name was Khan. She asks him to go tell the President that he is a Muslim and not a terrorist and not to come back till he is done so.
During his bus journey Rizwan repairs odds and ends for people and earns money. He also spends some time in a small town in Georgia at Mama Jenny’s.
Rizwan goes to a mosque to pray. He hears Dr. Faisal Rahman talking to a group of people. Rizwan tells him that he is not stating the facts right and that he is a liar. He then calls the FBI to report the Doctor. Next we see him at a rally for President Bush. He is screaming that his name is Khan and he is not a terrorist. The people around him hear the word terrorist and panic follows. The President is whisked away immediately and Rizwan is arrested. Apart from all the media there this incident also gets taped by two students who were at the rally. Rizwan is sent to prison where he is mentally and physically tortured. He says that he is scared and misses Mandira. The students pursue Khan’s story and gets one Bobby Ahuja to do a story on him. Rizwan story gets aired and is seen by the judge and also by a senator running for the presidency. The judge listens to Khan’s taped phone call to the FBI and Dr. Rahman gets arrested and Rizwan is freed. Rizwan sees Mandira but does not approach her since he has not fulfilled his promise to her. He hears that hurricane has hit Georgia and he sets off to rescue Mama Jenny. Rizwan’s supporters and the media are all puzzled over his disappearance. Later they find him in Georgia helping Mama Jenny and the folks there. The media airs his story and this is seen by everyone. Reece come forward and names the kids who were responsible for Sam’s death. Reece thanks Mandira for asking leniency for him. She replies that she didn’t do it for him; she did it for her friend Sarah. Sarah calls Mandira and asks her to go to Rizwan and not to lose him because of her anger. We see Mandira in Georgia and Rizwan is very happy to see her. Suddenly a man comes and stabs Rizwan and screams that he is responsible for Dr. Rahman’s arrest.
Rizwan wakes up in a hospital. He sees Mandira crying and reading his journal. She tells him she loves him and he says the same and asks her for a hug.
Rizwan is discharged from the hospital. He wants to go meet the new President. Mandira tells him that he doesn’t need to do so. He can come home now but he insists on fulfilling his promise.
We see him again trying to meet President, Barack Obama. This time he gets invited upon the stage to meet the President. He then tells the President that his name is Khan and he is not a terrorist. President Obama acknowledges this and sympathizes with Mandira on the death of her son. Rizwan also gives President the message from the homeland Security officer “Howdy”.
We see Rizwan and Mandira walking through the crowd as they cheer them.
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