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On the morning of July 9, Mohamed Atta rented a silver Hyundai Accent, which he booked from SIXT Rent-A-Car for July 9 to 16, and later extended to the 19th. He drove east out of Madrid towards the Mediterranean beach area of Tarragona. On the way, Atta stopped in Reus to pick up Ramzi bin al-Shibh at the airport. They drove to Cambrils, where they spent a night at the Hotel Monica. They checked out the next morning, and spent the next few days at an unknown location in Tarragona. The absence of other hotel stays, signed receipts or credit card stubs has led investigators to believe that the men may have met in a safe house provided by other al-Qaeda operatives in Spain. There, Atta and bin al-Shibh held a meeting to complete the planning of the attacks. Several clues have been found to link their stay in Spain to Syrian-born Imad Eddin Barakat Yarkas (Abu Dahdah), and Amer el Azizi, a Moroccan in Spain. They may have helped arrange and host the meeting in Tarragona. Yosri Fouda, who interviewed bin al-Shibh and Khalid Sheikh Mohammed (KSM) before the arrest, believes that Said Bahaji and KSM may have also been present at the meeting. Spanish investigators have said that Marwan al-Shehhi and two others later joined the meeting. Bin al-Shibh would not discuss this meeting with Fouda.

The hijacking began at 8:14 a.m. — 15 minutes after the flight departed — when beverage service would be starting. At this time, the pilots stopped responding to air traffic control, and the aircraft began deviating from the planned route. At 8:18 am, flight attendants Betty Ong and Madeline Amy Sweeney began making phone calls to American Airlines to report what was happening. Ong provided information about lack of communication with the cockpit, lack of access to the cockpit, and passenger injuries. At 8:24:38 a.m., a voice believed to be Atta's was heard by air traffic controllers, saying: "We have some planes. Just stay quiet and you will be OK. We are returning to the airport." "Nobody move, everything will be OK. If you try to make any moves you'll endanger yourself and the airplane. Just stay quiet." "Nobody move, please. We are going back to the airport. Don't try to make any stupid moves." The plane's transponder was turned off at 8:21 a.m. At 8:46:35 a.m., the plane flew into the North Tower of the World Trade Center.

On October 1, 2006, The Sunday Times released a video it had obtained "through a previously tested channel", purporting to show Mohamed Atta and Ziad Jarrah recording a martyrdom message six months earlier at a training camp in Afghanistan. The video, bearing the date of January 18, 2000, is of good resolution but contains no sound track. Lip readers have failed to decipher it. Atta and Jarrah appear in high spirits, laughing and smiling in front of the camera. They had never been pictured together before. Unidentified sources from both Al-Qaeda and the United States confirmed to The Times the video's authenticity. A separate section of the video shows Osama bin Laden addressing his followers at a complex near Kandahar. Ramzi bin al-Shibh is also identified in the video. According to The Sunday Times, "American and German investigators have struggled to find evidence of Atta's whereabouts in January 2000 after he disappeared from Hamburg. The hour-long tape places him in Afghanistan at a decisive moment in the development of the conspiracy when he was given operational command. Months later both he and Jarrah enrolled at flying schools in America."

In 2005, Army Lt. Col. Anthony Shaffer and Congressman Curt Weldon alleged that the Defense Department data mining project, Able Danger, produced a chart that identified Atta, along with Nawaf al-Hazmi, Khalid al-Mihdhar, and Marwan al-Shehhi, as members of a Brooklyn-based al-Qaeda cell in early 2000. Shaffer largely based his allegations on the recollections of Navy Captain, Scott Phillpott, who later recanted his recollection, telling investigators that he was "convinced that Atta was not on the chart that we had." Phillpott said that Shaffer was "relying on my recollection 100 percent," and the Defense Department Inspector General's report indicated that Philpott "may have exaggerated knowing Atta's identity because he supported using Able Danger's techniques to fight terrorism."

German investigators said that they had evidence that Mohamed Atta trained at al-Qaeda camps in Afghanistan from late 1999 to early 2000. The timing of the Afghanistan training was outlined on August 23, 2002, by a senior investigator. The investigator, Klaus Ulrich Kersten was the director of Germany's federal anticrime agency, the Bundeskriminalamt. He provided the first official confirmation that Atta and two other pilots had been in Afghanistan, and he also provided the first dates of the training. Kersten said in an interview at the agency's headquarters in Wiesbaden that Atta was in Afghanistan from late 1999 until early 2000, and that there was evidence that Atta met with Osama bin Laden there.

On June 6, 2002, ABC's World News Tonight broadcast an interview with Johnelle Bryant, former loan officer at the U.S. Department of Agriculture in south Florida, who told about her encounter with Mohamed Atta. This encounter took place "around the third week of April to the third week of May of 2000", before Atta's official entry date into the United States (see below). According to Bryant, Atta wanted to finance the purchase of a crop-duster. "He wanted to finance a twin-engine, six-passenger aircraft and remove the seats," Bryant told ABC's World News Tonight. He insisted that she write his name as ATTA, that he originally was from Egypt but had moved to Afghanistan, that he was an engineer and that his dream was to go to a flight school. He asked about the Pentagon and the White House. He said he wanted to visit the World Trade Center and asked Bryant about the security there. He mentioned Al Qaeda and said the organization "could use memberships from Americans". He mentioned Osama bin Laden and said "this man would someday be known as the world's greatest leader." Bryant said "the picture that came out in the newspaper, that's exactly what that man looked like." Bryant contacted the authorities after recognising Atta in news reports. Law-enforcement officials said Bryant passed a lie-detector exam.

During the Spain meetings, Atta and bin al-Shibh had coordinated the details of the attacks. The 9/11 Commission obtained details about the meeting, based on interrogations of Bin al-Shibh in the weeks after his arrest in September 2002. Bin al-Shibh explained that he passed along instructions from Osama bin Laden, including his desire for the attacks to be carried out as soon as possible. Bin Laden was concerned about having so many operatives in the United States. Atta confirmed that all the muscle hijackers had arrived in the United States, without any problems, but said that he needed five to six more weeks to work out details. Bin Laden also asked that other operatives not be informed of the specific data until the last minute. During the meeting, Atta and bin al-Shibh also decided on the targets to be hit, ruling out a strike on a nuclear plant. Bin al-Shibh passed along bin Laden's list of targets; bin Laden wanted the U.S. Capitol, the Pentagon, and the World Trade Center to be attacked, as they were deemed "symbols of America." If any of the hijackers could not reach their intended targets, Atta said, they were to crash the plane. They also discussed the personal difficulties Atta was having with fellow hijacker Ziad Jarrah. Bin al-Shibh was worried that Jarrah might even abandon the plan. The 9/11 Commission Report speculated that the now-convicted terrorist conspirator Zacarias Moussaoui was being trained as a possible replacement for Jarrah.

Records on Atta's cellphone indicated that he phoned the Moroccan embassy in Washington on January 2, just before Shehhi flew to the country. Atta flew to Spain on January 4, 2001, to coordinate with bin al-Shibh and returned to the United States on January 10. While in the United States he traveled to Lawrenceville, Georgia, where he and Shehhi visited a LA Fitness Health Club. During that time Atta flew out of Briscoe Field in Lawrenceville with a pilot, and Atta and either the pilot or Shehhi flew around the Atlanta area. They lived in the area for several months. On April 3, Atta and Shehhi rented a postal box in Virginia Beach, Virginia.

In July 2001, Atta again left for Spain in order to meet with bin al-Shibh for the last time. On July 7, 2001, Atta flew on Swissair Flight 117 from Miami to Zürich, where he had a stopover. On July 8, Atta was recorded on surveillance video when he withdrew 1700 Swiss francs from an ATM. He used his credit card to purchase two Swiss Army knives and some chocolate in a shop at the Zürich Airport. After the stopover in Zürich, he arrived in Madrid at 4:45 pm on Swissair Flight 656, and spent several hours at the airport. Then at 8:50 pm, he checked into the Hotel Diana Cazadora in Barajas, a town near the airport. That night and twice the next morning, he called Bashar Ahmad Ali Musleh, a Jordanian student in Hamburg who served as a liaison for bin al-Shibh.

From July 13 to 16, Atta stayed at the Hotel Sant Jordi in Tarragona. After bin al-Shibh returned to Germany on July 16, 2001, Atta had three more days in Spain. He spent two nights in Salou at the beachside Casablanca Playa Hotel, then spent the last two nights at the Hotel Residencia Montsant. On July 19, Atta returned to the United States, flying on Delta Air Lines from Madrid to Fort Lauderdale, via Atlanta.

On July 22, 2001, Atta rented a Mitsubishi Galant from Alamo Rent a Car, putting 3,836 miles on the vehicle before returning it on July 26. On July 25, Atta dropped Ziad Jarrah off at Miami International Airport for a flight back to Germany. On July 26, Atta traveled via Continental Airlines to Newark, New Jersey, checked into the Kings Inn Hotel in Wayne, New Jersey, and stayed there until July 30 when he took a flight from Newark back to Fort Lauderdale.

On September 10, 2001, Atta picked up Omari from the Milner Hotel in Boston, Massachusetts, and the two terrorists drove their rented Nissan Altima to a Comfort Inn in South Portland, Maine. On the way, they were seen getting gasoline at an Exxon gas station and visited the Longfellow House in Portland that afternoon; they arrived at the hotel at 5:43 p.m. and spent the night in Room 233. While in South Portland, they were seen making two ATM withdrawals and stopping at Wal-Mart. The FBI also reported that "two middle-eastern men" were seen in the parking lot of a Pizza Hut, where Atta is known to have eaten that day.

In the aftermath of the September 11, 2001 attacks, the names of the hijackers were released. There was some confusion regarding who Mohamed Atta was, and cases of mistaken identity. Initially, Mohamed Atta's identity was confused with that of a native Jordanian, Mahmoud Mahmoud Atta, who bombed an Israeli bus in the West Bank in 1986, killing one and severely injuring three. Mahmoud Atta was 14 years older than Atta. Mahmoud Atta, a naturalized U.S. citizen, was subsequently deported from Venezuela to the United States, extradited to Israel, tried and sentenced to life in prison. The Israeli Supreme Court later overturned his extradition and set him free. After 9/11, there also were reports stating that Mohamed Atta had attended International Officers School at Maxwell Air Force Base in Montgomery, Alabama. The Washington Post quoted a United States Air Force official who explained, "discrepancies in their biographical data, such as birth dates 20 years off, indicate we are probably not talking about the same people."

In the months following up to the September 11 attacks, officials at the Czech Interior Ministry asserted that Atta made a trip to Prague on April 8, 2001, to meet with an Iraqi intelligence agent named Ahmed Khalil Ibrahim Samir al-Ani. This piece of information was passed on to the FBI as "unevaluated raw intelligence". Intelligence officials have concluded that such a meeting did not occur. A Pakistani businessman named Mohammed Atta had come to Prague from Saudi Arabia on May 31, 2000, with this second Atta possibly contributing to confusion. The Egyptian Mohamed Atta arrived at the Florenc bus terminal in Prague, from Germany, on June 2, 2000. He left Prague the next day, flying on Czech Airlines to Newark, New Jersey, U.S. In the Czech Republic, some intelligence officials say the source of the purported meeting was an Arab informant who approached the Czech intelligence service with his sighting of Atta only after Atta's photograph had appeared in newspapers all over the world. United States and Czech intelligence officials have since concluded that the person seen with Ani was mistakenly identified as Atta, and the consensus of investigators has concluded that Atta never attended a meeting in Prague.

Atta's father, Mohamed el-Amir Awad el-Sayed Atta, a retired lawyer in Egypt, vehemently rejected allegations his son was involved in the September 11 attacks, and instead accused the Mossad and the United States government of having a hand in framing his son. Atta Sr. rejected media reports that stated his son was drinking wildly, and instead described his son as a quiet boy uninvolved with politics, shy and devoted to studying architecture. The elder Mr. Atta said he had spoken with Mohamed by phone the day after on September 12, 2001. He held interviews with the German news magazine Bild am Sonntag in late 2002, saying his son was alive and hiding in fear for his life, and that American Christians were responsible for the attacks. In a subsequent interview in 2005, Atta Sr. stated, "My son is gone. He is now with God. The Mossad killed him."

In June 2000, Atta and Marwan al-Shehhi arrived in the United States to learn how to pilot planes, obtaining instrument ratings in November. Beginning in May 2001, Atta assisted with the arrival of the muscle hijackers, and in July he traveled to Spain to meet with bin al-Shibh to finalize the plot. In August 2001, Atta traveled as a passenger on several "surveillance" flights, to establish in detail how the attacks could be carried out.

A video surfaced in October 2006. The first chapter of the video showed bin Laden at Tarnak Farms on January 8, 2000. The second chapter showed Atta and Ziad Jarrah reading their wills together ten days later on January 18. On his return journey, Atta left Karachi on February 24, 2000, by flight TK1057 to Istanbul where he changed to flight TK1661 to Hamburg. Immediately after returning to Germany, Atta, al-Shehhi, and Jarrah reported their passports stolen, possibly to discard travel visas to Afghanistan.

On March 22, 2000, Atta was still in Germany when he sent an e-mail to the Academy of Lakeland in Florida. He inquired about flight training, "Dear sir, we are a small group of young men from different Arab countries. Now, we are living in Germany since a while for study purposes. We would like to start training for the career of airline professional pilots. In this field, we haven't yet any knowledge but we are ready to undergo an intensive training program (up to ATP and eventually higher)." Atta sent 50–60 similar e-mails to other flight training schools in the United States.

According to official reports, Atta flew from Prague to Newark International Airport, arriving on June 3, 2000. That month, Atta and Shehhi stayed in hotels and rented rooms in New York City on a short-term basis. They continued to inquire about flight schools and personally visited some, including Airman Flight School in Norman, Oklahoma, which they visited on July 3, 2000. Days later, Shehhi and Atta ended up in Venice, Florida. Atta and Shehhi established accounts at SunTrust Bank and received wire transfers from Ali Abdul Aziz Ali, Khalid Sheikh Mohammed's nephew in the United Arab Emirates. On July 6, 2000, Atta and Shehhi enrolled at Huffman Aviation in Venice, where they entered the Accelerated Pilot Program, while Ziad Jarrah took flight training from a different school also based in Venice. When Atta and Shehhi arrived in Florida, they initially stayed with Huffman's bookkeeper and his wife in a spare room of their house. After a week, they were asked to leave because they were rude. Atta and Shehhi then moved into a small house nearby in Nokomis where they stayed for six months.

Atta began flight training on July 6, 2000, and continued training nearly every day. By the end of July, both Atta and Shehhi did solo flights. Atta earned his private pilot certificate in September, and then he and Shehhi decided to switch flight schools. Both enrolled at Jones Aviation in Sarasota and took training there for a brief time. They had problems following instructions and were both very upset when they failed their Stage 1 exam at Jones Aviation. They inquired about multi-engine planes and told the instructor that "they wanted to move quickly, because they had a job waiting in their country upon completion of their training in the U.S." In mid-October, Atta and Shehhi returned to Huffman Aviation to continue training. In November 2000, Atta earned his instrument rating, and then a commercial pilot's license in December from the Federal Aviation Administration.

Atta continued with flight training that included solo flights and simulator time. On December 22, Atta and Shehhi applied to Eagle International for large jet and simulator training for McDonnell Douglas DC-9 and Boeing 737-300 models. On December 26, Atta and Shehhi needed a tow for their rented Piper Cherokee on a taxiway of Miami International Airport after the engine shut down. On December 29 and 30, Atta and Marwan went to the Opa-locka Airport where they practiced on a Boeing 727 simulator, and they obtained Boeing 767 simulator training from Pan Am International on December 31. Atta purchased cockpit videos for Boeing 747-200, Boeing 757-200, Airbus A320 and Boeing 767-300ER models via mail-order from Sporty's Pilot Shop in Batavia, Ohio, in November and December 2000.

In late 1999, Atta, Shehhi, Jarrah, Bahaji, and bin al-Shibh decided to travel to Chechnya to fight against the Russians, but were convinced by Khalid al-Masri and Mohamedou Ould Slahi at the last minute to change their plans. They instead traveled to Afghanistan over a two-week period in late November. On November 29, 1999, Mohamed Atta boarded Turkish Airlines Flight TK1662 from Hamburg to Istanbul, where he changed to flight TK1056 to Karachi, Pakistan. After they arrived, they were selected by Al Qaeda leader Mohammed Atef as suitable candidates for the "planes operation" plot. They were all well-educated, had experience of living in western society, along with some English skills, and would be able to obtain visas. Even before bin al-Shibh had arrived, Atta, Shehhi, and Jarrah were sent to the House of Ghamdi near bin Laden's home in Kandahar, where he was waiting to meet them. Bin Laden asked them to pledge loyalty and commit to suicide missions, which Atta and the other three Hamburg men all accepted. Bin Laden sent them to see Atef to get a general overview of the mission, and then they were sent to Karachi to see Khalid Sheikh Mohammed to go over specifics.

By mid-1998, Atta was no longer eligible for university housing in Centrumshaus. He moved into a nearby apartment in the Wilhelmsburg district, where he lived with Said Bahaji and Ramzi bin al-Shibh. By early 1999, Atta had completed his thesis, and formally defended it in August 1999.

In mid-1998, Atta worked alongside Shehhi, bin al-Shibh, and Belfas, at a warehouse, packing computers in crates for shipping. The Hamburg group did not stay in Wilhelmsburg for long. The next winter, they moved into an apartment at Marienstrasse 54 in the borough of Harburg, near the Hamburg University of Technology, at which they enrolled. It was here that the Hamburg cell developed and acted more as a group. They met three or four times a week to discuss their anti-American feelings and to plot possible attacks. Many al-Qaeda members lived in this apartment at various times, including hijacker Marwan al-Shehhi, Zakariya Essabar, and others.

After leaving Plankontor in the summer of 1997, Atta disappeared again and did not return until 1998. He had made no progress on his thesis. Atta phoned his graduate advisor, Machule, and mentioned family problems at home, saying, "Please understand, I don't want to talk about this." At the winter break in 1997, Atta left and did not return to Hamburg for three months. He said that he went on pilgrimage to Mecca again, just 18 months after his first time. This claim has been disputed; Terry McDermott has argued that it is unusual for someone to go on pilgrimage so soon after the first time and to spend three months there (more than Hajj requires). When Atta returned, he claimed that his passport was lost and applied for a new one, which is a common tactic to erase evidence of travel to places such as Afghanistan. When he returned in spring 1998, after disappearing for several months, he had grown a thick long beard, and "seemed more serious and aloof" than before to those who knew him.

Mohamed Atta varied his name on documents, also using "Mehan Atta", "Mohammad El Amir", "Muhammad Atta", "Mohamed El Sayed", "Mohamed Elsayed", "Muhammad al-Amir", "Awag Al Sayyid Atta", and "Awad Al Sayad". In Germany, he registered his name as "Mohamed el-Amir Awad el-Sayed Atta", and went by the name Mohamed el-Amir at the Hamburg University of Technology. In his will, written in 1996, Atta gives his name as "Mohamed the son of Mohamed Elamir awad Elsayed". Atta also claimed different nationalities, sometimes Egyptian and other times telling people he was from the United Arab Emirates.

On April 11, 1996, Atta signed his last will and testament at the mosque, officially declaring his Muslim beliefs and giving 18 instructions regarding his burial. This was the same day that Israel, much to the outrage of Atta, attacked Lebanon in Operation Grapes of Wrath; signing the will "offering his life" was his response. The instructions in his last will and testament reflect both Sunni funeral practices along with some more puritanical demands from Salafism, including asking people not "to weep and cry" and to generally refrain from showing emotion. The will was signed by el-Motassadeq and a second person at the mosque.

On August 1, 1995, Atta returned to Egypt for three months of study. Before this trip he grew out a beard, with a view to show himself as a devout Muslim and to make a political gesture thereby. Atta returned to Hamburg on October 31, 1995, only to join the pilgrimage to Mecca shortly thereafter.

On August 6, Atta and Shehhi rented a white, four door 1995 Ford Escort from Warrick's Rent-A-Car, which was returned on August 13. On August 6, Atta booked a flight on Spirit Airlines from Fort Lauderdale to Newark, leaving on August 7 and returning on August 9. The reservation was not used and canceled on August 9 with the reason "Family Medical Emergency". Instead, he went to Central Office & Travel in Pompano Beach to purchase a ticket for a flight to Newark, leaving on the evening of August 7 and schedule to return in the evening on August 9. Atta did not take the return flight. On August 7, Atta checked into the Wayne Inn in Wayne, New Jersey and checked out on August 9. The same day, he booked a one-way first class ticket via the Internet on America West Flight 244 from Ronald Reagan Washington National Airport to Las Vegas. Atta traveled twice to Las Vegas on "surveillance flights" rehearsing how the 9/11 attacks would be carried out. Other hijackers traveled to Las Vegas at different times in the summer of 2001.

Atta's professor, Dittmar Machule, brought him along on an archaeological expedition to Aleppo in 1994. The invitation had been for a three-day visit, but Atta ended up staying several weeks that August, only to visit Aleppo yet again that December. While in Syria, he met Amal, a young Palestinian woman who worked for a planning bureau in the city. Volker Hauth, who was traveling with Atta, described Amal as "attractive and self-confident. She observed Muslim customs, taking taxis to and from the office so as not to come into close physical contact with men on buses. But she was also said to be 'emancipated' and 'challenging'. Atta and Amal appeared to be attracted to each other, but Atta soon decides that "she had a quite different orientation and that the emancipation of the young lady did not fit." His nascent infatuation with her, begrudgingly realised, was the closest thing Atta knew to romance. In mid-1995, he stayed for three months in Cairo, on a grant from the Carl Duisberg Society, along with fellow students Volker Hauth and Ralph Bodenstein. The academic team inquired into the effects of redevelopment in the Islamic Cairo, the old quarter, which the government undertook to remodel for tourism. Atta stayed in Cairo awhile with his family after Hauth and Bodenstein flew back to Germany.

By early 1993, Atta had moved into university housing with two roommates, in Centrumshause. He stayed there until 1998. During that period, his roommates grew annoyed with him. He seldom bathed, and they could not bear his "complete, almost aggressive insularity". He kept to himself to such an extent that he would turn away from a salutation with supercilious silence.

Atta graduated from Cairo University with marks insufficient for the graduate program. As his father insisted that he go abroad for graduate studies, Atta, to this end, entered a German-language program at the Goethe Institute in Cairo. In 1992, his father had overheard a German couple who were visiting Egypt's capital. The couple explained at dinner that they ran an exchange program and invited Atta to continue his studies in Germany; they also offered him room and board at their home in the city. Mohamed Atta accepted and was in Germany two weeks later, in July.

While in Hamburg, Atta held several positions, such as one part-time job at Plankontor, as well as another at an urban planning firm, beginning in 1992. He was let go from the firm in 1997, however, because its business had declined and "his draughtsmanship was not needed" after it bought a CAD system. Among other odd jobs to supplement his income, Atta sometimes worked at a cleaning company and sometimes bought and sold cars. Atta had harbored a desire to return to his native city, ever since he finished his studies in Hamburg; but he was prevented by the dearth of job prospects in Cairo, his family lacking the "right connections" to avail the customary nepotism. Further, after the Egyptian government had imprisoned droves of political activists, he knew better than to trust it not to target him too, with his social and political beliefs being such as they were.

After coming to Hamburg in 1992, Atta grew more religiously fanatical and frequented the mosque with greater regularity. His friends in Germany described him as an intelligent man in whom religious convictions and political motives held equal sway. He harbored anger and resentment toward the U.S. for its policy in Islamic nations of the Middle East, with nothing inflaming his ire more than the Oslo Accords and the Gulf War in particular. He was also angry and bitter at the elite in his native Egypt, who hoarded all the power for themselves, as well as at the Egyptian government, that cracked down on the dissident Muslim Brotherhood.

Born and raised in Egypt, Atta studied architecture at Cairo University, graduating in 1990, and continued his studies in Germany at the Hamburg University of Technology. In Hamburg, Atta became involved with the al-Quds Mosque, where he met Marwan al-Shehhi, Ramzi bin al-Shibh, and Ziad Jarrah, together forming the Hamburg cell. Atta disappeared from Germany for periods of time, embarking on the hajj in 1995 but also meeting Osama bin Laden and other top al-Qaeda leaders in Afghanistan from late 1999 to early 2000. Atta and the other Hamburg cell members were recruited by bin Laden and Khalid Sheikh Mohammed for a "planes operation" in the United States. Atta returned to Hamburg in February 2000, and began inquiring about flight training in the United States.

At the Hamburg University of Technology, Atta studied under the guidance of the department chair, one Dittmar Machule, who specialized in the Middle East. Atta was averse to modern development. This included the construction of high-rise buildings in Cairo and other ancient cities in the region. He believed that the drab and impersonal apartment blocks, built in the 60s and 70s, ruined the beauty of old neighborhoods and robbed their people of privacy and dignity. Atta's family moved into one such eyesore in 1990; it was to him but "a shabby symbol of Egypt's haphazard attempts to modernize and its shameless embrace of the West." For his thesis, Atta concentrated on the ancient Syrian city of Aleppo. He researched the history of the urban landscape in relation to the general theme of conflict between Arab and modern civilization. He criticized how the newfangled skyscrapers and other modernizing projects were disrupting the fabric of communities by blocking common streets and altering the skyline.

When Atta was ten, his family moved to the Cairo neighborhood of Abdeen, situated near the city center. His father, who kept the family ever insulated, forbade young Atta to fraternize with the other children in their neighborhood. Having little else to do, he mostly studied at home and easily excelled in school. In 1985, Atta enrolled at Cairo University and focused his studies on engineering. He was among the highest-scoring students; by his senior year, he was admitted to an exclusive architecture program. After he graduated in 1990 with an architecture degree, he joined the Engineers Syndicate, an organization under the control of the Muslim Brotherhood. He then worked for several months at the Urban Development Center in Cairo, where he joined various building projects and dispatched diverse architectural tasks. Also in 1990, Atta's family moved into the eleventh floor of an apartment building in the Egyptian city of Giza.

Mohamed Mohamed el-Amir Awad el-Sayed Atta (/ˈ æ t ɑː / AT -ah; Arabic: محمد محمد الأمير عوض السيد عطا ‎ Muḥammad Muḥammad al-Amir 'Awaḍ as-Sayyid 'Aṭā  [mæˈħæmmæd elʔæˈmiːɾ ˈʕɑwɑdˤ esˈsæj.jed ˈʕɑtˤɑ] ; September 1, 1968 – September 11, 2001) was an Egyptian hijacker and one of the ringleaders of the September 11 attacks in which four United States commercial aircraft were commandeered with the intention of destroying specific civilian and military targets. He served as the hijacker-pilot of American Airlines Flight 11 which he crashed into the North Tower of the World Trade Center as part of the coordinated attacks. At 33 years of age, he was the oldest of the 19 hijackers who took part in the attacks.

Atta was born on September 1, 1968, in Kafr el-Sheikh, located in Egypt's Nile Delta region. His father, Mohamed el-Amir Awad el-Sayed Atta, was a lawyer, educated in both sharia and civil law. His mother, Bouthayna Mohamed Mustapha Sheraqi, came from a wealthy farming and trading family and was also educated. Bouthayna and Mohamed married when she was 14, via an arranged marriage. The family had few relatives on the father's side and kept their distance from Bouthayna's family. In-laws characterized Atta's father as "austere, strict, and private," and neighbors viewed the family as reclusive. Atta was the only son; he had two older sisters who are both well-educated and successful in their careers — one as a medical doctor and the other as a professor.

Atta and Omari arrived early the next morning, at 5:40 a.m., at Portland International Jetport, where they left their rental car in the parking lot and boarded a 6:00 a.m. Colgan Air (US Airways Express) BE-1900C flight to Boston's Logan International Airport. In Portland, Mohamed Atta was selected by the Computer Assisted Passenger Prescreening System (CAPPS), which required his checked bags to undergo extra screening for explosives but involved no extra screening at the passenger security checkpoint.