Flight MH653 departed Penang's Runway 22 at exactly 19:21 hours for Kuala Lumpur's Subang Airport (now known as Sultan Abdul Aziz Shah Airport).Passengers included the Malaysian Agricultural Minister, Dato' Ali Haji Ahmad; Public Works Department Head, Dato' Mahfuz Khalid; and Cuban Ambassador to Japan, Mario García. The pilot in command was Captain G.K. Ganjoor. The aircraft crashed at Tanjong Kupang.
At approximately 19:54 hours, while at an altitude of 4,000 feet over Batu Arang and descending toward Subang's Runway 33, captain G.K. Ganjoor reported an "unidentified hijacker" onboard to Subang Tower. The tower immediately notified the authorities, who made emergency preparations at the airport.
A few minutes later, however, Captain Ganjoor radioed: "We're now proceeding to Singapore...". Flight MH653 never touched down at Singapore.
The cockpit voice recordings indicate noises suggestive of the cockpit door being broken in, along with a reasonable amount of screaming and cursing. No noises are heard from within the cockpit to indicate any of the three occupants were conscious. The autopilot was then disconnected, possibly due to a pitch input by someone entering the cockpit and trying to control the aircraft. An investigator speculated that someone pulled back on the column, causing a pitch up, followed by an oscillation. This rapidly developed into a high amplitude phugoid oscillation that resulted in a rapid dive.
At 20:15 hours, all communication with flight MH653 was lost.
At 20:36 hours, the residents of Kampong Ladang, Tanjong Kupang in Johor reported hearing explosions and seeing burning wreckage in a swamp. The wreckage was later identified as Flight MH653. The plane hit the ground at a near-vertical angle at a very high speed. There were no survivors and not one recognizable body was found.
After the incident, the Aviation Security Unit of the Airport Standard Division of the Department of Civil Aviation Malaysia was established.
Airlines began using improved technology and safety systems more widely to reduce incidences of hijacked aircraft.Some speculate that the Japanese Red Army was responsible for the hijacking, although no further evidence to support this hypothesis has come forward.All recovered remains were x-rayed in an attempt to discover evidence of a projectile or weapon. No weapon or bullet was ever found. The victims' remains were interred in a mass burial