On October 31, 1999, the Boeing 767-300ER operating the route crashed into the Atlantic Ocean about 60 miles (100 km) south of Nantucket Island, Massachusetts, killing all 217 passengers and crew on board, making it the deadliest aviation disaster for EgyptAir, and also the second-deadliest aviation accident involving a Boeing 767 aircraft, behind Lauda Air Flight 004.

[3][4] However the NTSB continues to dispute the findings of the ECAA report, claiming that there is no possible explanation for the flight's final movements, other than an intentional human act.

The autopilot-disengagement warning was not heard on the CVR, indicating that the autopilot was disengaged manually,[b] and, for the next 10 seconds, the aircraft remained in straight and level flight.

At 1:49:53, the throttles of both engines were moved to idle, and, 1 second later, the aircraft entered an increasingly steep dive, resulting in weightlessness (zero-g) throughout the cabin.

Radar data indicated that, at approximately 1:50:38, the aircraft entered a steep climb, presumably due to the abrupt maneuvers made by the flightcrew to recover from the dive.

At some point during the final descent, the left engine and some other small pieces of debris separated from the aircraft due to the extreme structural stresses produced during the dive.

[3] The aircraft, like all commercial airliners, was equipped with a Mode C transponder, which automatically reported the plane's altitude when queried by the ATC radar.

[3] Several subsequent "primary" returns (simple radar reflections without the encoded Mode C altitude information) were received by ATC, the last being at 06:52:05.

[16][17] At sunrise, the United States Merchant Marine Academy training vessel T/V Kings Pointer found an oil sheen and some small pieces of debris.

Rescue efforts continued by air and by sea, with a group of U.S. Coast Guard cutters covering 10,000 sq mi (26,000 km2) on October 31, 1999, with the hope of locating survivors, but no bodies were recovered from the debris field.

Atlantic Strike Team members brought two truckloads of equipment from Fort Dix, New Jersey, to Newport, Rhode Island, to set up an incident command post.

[21] Osama El-Baz, an adviser to Egyptian President Hosni Mubarak, said, "This pilot can't know anything about the plane; the chances that he has any information [about the crash of Flight 990] are very slim.

[27] American investigators confirmed key aspects of Taha's information, but decided not to anger the Egyptian government further by issuing any official statement about Al-Batouti's motive.

[25][28] EgyptAir terminated Taha's employment,[29] and his application for British asylum was reportedly declined,[21] though he gave an extensive 2002 newspaper interview in London[28] and was featured in a 2005 documentary.

The accident airplane's movements after the command captain returned to the cockpit were the result of both pilots' inputs, including opposing elevator inputs where the relief first officer continued to command nose-down and the captain commanded nose-up elevator movements.From the NTSB report's "Probable Cause" section: The National Transportation Safety Board determines that the probable cause of the EgyptAir flight 990 accident is the airplane's departure from normal cruise flight and subsequent impact with the Atlantic Ocean as a result of the relief first officer's flight control inputs.

The ECAA report concluded that "the Relief First Officer did not deliberately dive the airplane into the ocean" and that mechanical failure was "a plausible and likely cause of the accident".

"[30] The NTSB investigation and its results drew criticism from the Egyptian government, which advanced several alternative theories about mechanical malfunction of the aircraft.

In this state, one side of the elevator is up and the other down; on the 767, this condition is only possible through flight control input (i.e., one yoke is pushed forward, the other pulled backward).

[3] Some evidence indicated that one of the right elevator's power control units may have suffered a malfunction, and the Egyptian investigation mentioned this as a likely cause of the crash.

[4] While noting that the damage did indeed exist, the NTSB countered that it was more likely a result of the crash rather than a pre-existing problem, as the 767 is designed to remain airworthy even with two PCUs failed.

Long before the NTSB issued its final report, Western media began to speculate about the meaning of the recorded cockpit conversations and about possible motives – including suicide and terrorism – behind Al-Batouti's actions on the flight.

The speculation, in part, was based on leaks from an unnamed federal law-enforcement official that the crew member in the co-pilot's seat was recorded as saying, "I made my decision now.

"[31] During a press conference held on November 19, 1999, NTSB chairman Jim Hall denounced such speculation, and said that it had "done a disservice to the long-standing friendship between the people of the United States of America and Egypt.

[32] It is believed that the speculation arose from a mistranslation of an Egyptian Arabic phrase (Tawkalt ala Allah) meaning "I rely on God.

[33] The unprecedented presence of 33 members of the Egyptian general staff on the flight (contrary to standard operating procedure) fed a number of conspiracy theories.

[32] Unifying all the Egyptian press was a stridently held belief that "it is inconceivable that a pilot would kill himself by crashing a jet with 217 people aboard.

'It is not possible that anyone who would commit suicide would also kill so many innocent people alongside him,' said Ehab William, a surgeon at Cairo's Anglo-American Hospital.

[38][39] Al Jazeera, an Arabic-language channel state sponsored by Qatar, produced a documentary by Yosri Fouda about the flight that was broadcast in March 2000.

No scenario that the Egyptians came up with, or that we came up with, in which there were some sort of mechanical failure in the elevator control system, would either match the flight profile or was a situation in which the airplane was not recoverable.

In interviews conducted for the program, the relief first officer's family members vehemently disputed the suicide and deliberate crash theories, and dismissed them as biased.