Colonel Jacinto Ligot was the chief of the Philippine Air Force rescue team, which faced difficulties due to the deep ravines and dense vegetation on the slopes of the mountain. The pilots were flying visually not instrumentally when the plane vanished from radar. While the skies were clear at the airport, the mountains may have been covered by fog. Chief of Staff General Clemente Mariano speculated that the plane "almost cleared the top of the mountain, but it may have suffered a down-draft, causing it to hit the mountain."

The plane left Manila at 0100 GMT and was scheduled to arrive at 0303 GMT in Cagayan de Oro. The plane made a stop at Tacloban on 0220 GMT, though sources differ about whether it was a scheduled or unscheduled stop. According to one source, the fight made an unscheduled stop at Tacloban to deliver a needed airplane tire for another Cebu Pacific airplane in Tacloban. The last contact was 15 minutes before the plane was due to land, with the airport tower. In that call, the pilot said he was 68 kilometres (42 mi) from the airport and was starting to descend. There was no indication that the plane was in trouble. The plane crashed 45 kilometres (28 mi) away from the airport.

The plane carried five crew members and 99 Filipino passengers, including five children. Five passengers were from Australia, Austria, Japan, Switzerland and Canada.

The cause of the crash is still a source of controversy in the Philippines. Jesus Dureza, the crisis manager during the rescue and retrieval operations, said he found out the CAAP (then ATO) maps used by the pilots listed the elevation of Mt. Sumagaya at 5,000 feet above sea level, while the mountain actually is 6,000 feet above sea level. This error might have misled the pilots to believe that they were clear of terrain, while in fact they were flying dangerously low. The ATO, on the other hand, pointed out in its official report deficiencies in the training of the pilots