When Chuck returns home, Kelly reveals that it was never discovered exactly what caused the aircraft to crash, but that it was possibly some mislabeled hazardous material in the cargo that ignited. From the evidence provided in the film, there are a few possibilities. First, we get a glimpse of the weather head-up-display prior to the crash; it is easy to see that the aircraft is surrounded by hazardous weather and turbulence. Second, we can see, through the cockpit windows, a brewing lightning storm. Chuck is quite literally sucked out of the lavatory, a tell-tale sign of a loss of cabin pressure. This means that the integrity of the structure of the aircraft was breached. As the aircraft is making its final mayday calls before plunging into the Pacific, we hear the pilots indicate an engine fire (if not multiple engine fires). In summary, we can assume that the aircraft's structural integrity was breached, resulting in a loss of cabin pressure, and that something incited an engine fire (this could be a number of things, anything from Kelly's hypothesis to a lightning strike on the aircraft). A lightning strike or electrical spark from the storm is more probable than a "mislabeled cargo container." Cargo, hazardous and non-hazardous, are transported separately and handled in an entirely different process. Also, after the cabin depressurization, at least two pallets of cargo shifted dramatically, which would greatly affect the plane's center of gravity. Cargo is always loaded by a formula which ensures the plane is balanced. Pallets shifting as they did in the movie might make the aircraft un-flyable, possibly causing a catastrophic nose dive. An engine fire in and of itself wouldn't necessarily cause it to nose dive into the ocean. In the end, severe weather, turbulence, and disorientation were secondary contributing factors to the crash.