The flight, on HB-IWF, an MD-11, departed John F. Kennedy Airport at 21:18 (ADT) with 215 passengers and 14 crew enroute to Geneva. The flight crew smelt smoke in the cockpit from around 22:00. Around fifteen minutes later smoke was visible in the cockpit and a number of systems were failing, the pilot announced a "pan pan" and requested a diversion to Boston's Logan International Airport, but was instead directed to the closer Halifax International Airport in Enfield, Nova Scotia, 56 nm away. At 22:21 the pilot reduced altitude from 10,000 m to 3,000 m and announced he was dumping fuel. At 22:24 he finally declared an emergency, contact with the aircraft was lost one minute later and it struck the ocean at around 22:31.
Flight recorders were quickly retrieved (FDR on September 6 and CVR on September 11, 1998) and 78 recovered bodies were identified. By October, 1998 the cause of the crash was generally believed to be due to faulty wiring in the cockpit and certain groups issued Aviation Safety Recommendations. The Canadian Transportation Safety Board (TSB) did not release its preliminary report until August 30, 2000 and the final report was delayed until 2003.
The final phase of wreckage recovery by dredging ended in December, 1999 with around 2 million pieces of the aircraft and its contents recovered, 98% of the aircraft was retrieved from 50-60 m deep. The investigation identified the cause of the crash as originating in a fire in the right side cockpit overhead controls. Arcing from wiring of the in-flight entertainment network did not trip the circuit breakers but ignited flammable covering on insulation blankets and quickly spread across other flammable materials. The crew did not recognise that a fire had started and were not warned by instruments, and reacting to an uncertain problem, the crew's ability to control the aircraft was soon overcome as the rapid spread of the fire led to the failure of key display systems. The TSB concluded that even if they had been aware of the nature of the problem the rate of spread of the fire would have precluded a safe landing at Halifax even if an approach had begun as soon as the 'pan pan' was declared.
The TSB made nine recommendations relating to changes in aircraft materials, electrical systems and flight data capture (both flight recorders had halted operations six minutes before impact). General recommendations were also made regarding improvements in checklists, fire detection and fire-fighting equipment.
In September, 1999 Swissair and Boeing offered the families of the passengers full compensatory damages. This was rejected in favor of a $19.8 billion suit against Swissair and DuPont, the supplier of mylar insulation sheathing.
A number of famous or semi-famous people died in this accident, including Jake LaMotta Jr, son of former boxing world champion Jake LaMotta. A number of works of art, including pieces by Pablo Picasso, were lost in the crash.
A memorial to the victims has since been established at Peggy's Cove.