The trouble originated in one of the aircraft's three air data inertial reference units, known as ADIRUs, which began feeding corrupt data to the flight control computer. At 12:42:27, the A330 pitched violently nose-down without any command from the pilots, reaching 8.4 degrees pitch-down and subjecting the cabin to negative 0.8 g. The aircraft plummeted 650 feet in seconds. Passengers not wearing seatbelts were thrown into the ceiling. Overhead bins burst open, showering the cabin with luggage. Sullivan fought the controls and recovered the aircraft to its assigned altitude, FL370, within twenty seconds. Then, at 12:45:08, it happened again: a second uncommanded pitch-down, this time 3.5 degrees, dropping the aircraft another 400 feet. The pilots recovered in sixteen seconds. Two brief, violent episodes, separated by less than three minutes, that left the cabin looking like it had been hit by a tornado.

Sullivan initially declared a pan-pan, the level below a full emergency. When reports from the cabin reached the cockpit describing the extent of injuries, fractures, spinal damage, lacerations, people unable to move, he upgraded to mayday. The nearest suitable airfield was Learmonth Airport, a Royal Australian Air Force base near the remote town of Exmouth on Western Australia's North West Cape. Sullivan diverted and landed safely. On the ground, the Royal Flying Doctor Service and a CareFlight jet ambulance were waiting. Fourteen of the most seriously injured passengers and crew were airlifted to Perth. In total, one crew member and eleven passengers suffered serious injuries, while eight crew members and ninety-nine passengers sustained minor injuries. Qantas sent two additional aircraft from Perth carrying medical teams and customs officers to care for the remaining passengers.

The Australian Transport Safety Bureau's investigation, supported by the French Bureau of Enquiry and Analysis, Airbus, and the European Aviation Safety Agency, identified a fault in the number-one ADIRU as the likely origin. The unit had begun transmitting erroneous data spikes to the flight control primary computer, which interpreted them as valid sensor readings and commanded the pitch-down maneuvers. What made the incident particularly alarming was the discovery of a previously unknown software design limitation in the A330's fly-by-wire system: the flight control computer did not adequately filter out the type of data corruption the ADIRU was producing. In January 2009, the European Aviation Safety Agency issued an emergency airworthiness directive for all A330 and A340 aircraft equipped with Northrop Grumman ADIRUs. The definitive trigger for the ADIRU malfunction was never conclusively established, though investigators believed a marginal hardware weakness made the unit susceptible to some environmental factor.

Behind the technical findings were human consequences that took years to unfold. Qantas offered compensation to passengers including full refunds, travel vouchers equivalent to a return trip to London, and medical expense coverage. Several passengers pursued legal action. Flight attendant Fuzzy Maiava was permanently injured, left unable to work or drive. He was advised not to accept Qantas's offered NZ$35,000 settlement so he could join a class-action lawsuit against Airbus and Northrop Grumman. The case was dismissed on procedural grounds, leaving Maiava with nothing. Diana Casey, an off-duty Qantas customer service manager who was herself injured but helped numerous passengers during the emergency, was later banned by Qantas from giving interviews about the incident. Sullivan eventually wrote a book, published in 2019, titled No Man's Land: The Untold Story of Automation and QF72, examining the broader questions the incident raised about human pilots and automated systems.

QF72 became a case study in the tension between automation and human control. The fly-by-wire system that was supposed to protect the aircraft from dangerous maneuvers instead caused them, overriding the flight envelope protections that pilots are taught to trust. Sullivan's ability to recover the aircraft both times, fighting against a computer that was actively working against him, demonstrated why human pilots remain essential even in the most automated cockpits. The incident was dramatized in the Canadian television series Mayday in 2018 and drew commentary from Chesley Sullenberger, the captain of US Airways Flight 1549. The aircraft itself, VH-QPA, sustained only minor damage and was repaired and returned to service. The people aboard were not so easily fixed. For the passengers who were flung into the ceiling of an aircraft at 37,000 feet over the Indian Ocean, the scars, physical and otherwise, proved far more lasting than a software patch.