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 months following 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 the 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 is 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."