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The 24-year-old was shot in the chest at a petrol station on Wednesday night and the assailants drove off in his vehicle.
The hijacked vessel was intercepted on Thursday, the Navy said.
The incident of hijacking of the cargo ship MV Lila Norfolk was reported on Thursday by the UK Maritime Trade Operations (UKMTO).
The NIA said that Salla intentionally put the printed threat letter inside the toilet to disrupt the aircraft operation thus jeopardising the safety of the passengers and the crew members on board.
Security forces stormed the plane and detained the lone hijacker and evacuated all the passengers safely.