Murder, drugs and a pregnancy secret are part of a hush-hush cover-up that’s been exposed on the 15-year anniversary of John F. Kennedy Jr.’s tragic plane crash.

Authorities cited “pilot error” for the July 16, 1999, accident, which took the lives of the “George” magazine editor, 38, his wife, Carolyn Bessette, 33, and her sister, Lauren, 34.

But The National ENQUIRER has learned that the FBI theorized either a bomb was aboard Kennedy’s Piper Saratoga plane or the aircraft was brought down by something fired from a boat. Kennedy and his wife were heading to a cousin’s wedding in Cape Cod from New Jersey. They had first planned to drop off her sister in Martha’s Vineyard, Mass.

But Kennedy, a novice pilot, crashed his plane into the ocean while approaching the tiny airport. All three aboard perished.

Fifteen years later, investigative commentator Michael Rivero says: “I am certain it was an assassination and cover-up!”

The ENQUIRER has also learned “suspicious individuals had previously been seen lurking around his (Kennedy’s) plane” at New Jersey’s Essex County Airport. The FBI also discovered “suspicious boating activity” in the area where the plane made its final approach to the Vineyard airport.

But before the FBI could complete its probe, it was mysteriously halted. The ENQUIRER has reported JFK Jr.’s uncle – the late Sen. Ted Kennedy – was behind “a cover-up” launched to prevent secrets from being exposed about his famous nephew.

A source said: “Ted ordered the Navy to destroy photos and videos – and had their autopsies rushed to prevent any findings that could have shown Carolyn was pregnant or on drugs.”

As The ENQUIRER has reported, Carolyn had used cocaine. The three victims’ cremations were so rushed that, while John was worth a reported $100 million, his remains had to be placed in a cardboard box for the $175 cremation. Gwen Kopechne, whose daughter died when she was a passenger in Ted’s car in the 1969 Chappaquiddick, Mass. accident, has told The ENQUIRER : “Ted Kennedy is covering up the plane crash the same way he covered up the death of my daughter Mary Jo.”

The Bessettes’ heartbroken mother, Ann Freeman, remains too grief-stricken to talk.