The album features multiple lyrical themes: religion, politics and warfare, as well as Mustaine's personal issues, such as his fight against drug and alcohol addiction, UFO conspiracy theories and even the Marvel Comics character Punisher.
The opening song, "Holy Wars... The Punishment Due" finds its thematic inspiration derived from the Northern Ireland conflict, in which the largely Catholic nationalist community were in conflict with the mainly Protestant loyalist community over the sovereignty of the six counties of Northern Ireland. Mustaine has said that at a show in Antrim, Northern Ireland, he discovered bootlegged Megadeth T-shirts were on sale. He was dissuaded from taking action to have them removed on the basis that they were part of fund raising activities for "The Cause", explained as something to bring equality to Catholics and Protestants in the region. Liking how "The Cause" sounded as was explained to him, Mustaine dedicated a performance of "Anarchy in the U.K." to it, causing the audience to riot. The band were escorted in a bulletproof bus back to their hotel in Dublin after the show. This incident, along with Marvel's Punisher, inspired Mustaine to write the song.
"Rust in Peace... Polaris", addresses the topic of nuclear warfare, with "Polaris" referring to the Cold War-era Lockheed UGM-27 Polaris intercontinental ballistic missile. Mustaine has revealed that the song, originally titled "Child Saint", was one of his earlier compositions, having been written before his tenure with Metallica (1981–83). Menza proposed the concept for "Hangar 18", a song about UFO conspiracies and Area 51. Musically, the song features twin guitar solos after the verse.
In 2017, more than 25 years after the album was released, Dave Mustaine revealed the majority of "Holy Wars" tabs on the web did not transcribe the main riff correctly, and posted the correct transcription himself.
The tracks "Holy Wars... The Punishment Due" and "Hangar 18" have become staples of Megadeth's live set, and are fan favorites. The guitar solo on "Tornado of Souls" is considered to be one of the greatest solos in heavy metal music. In 2010, the band announced a 22-show North American tour to celebrate the 20th anniversary of Rust in Peace. The band performed the entire album at every show. Dates in South and Central America were later added to the tour, due to positive response from fans. In 2010, Shout! Factory released a live recording filmed on the Hollywood Palladium stop of the tour, entitled Rust in Peace Live. It was released on September 7, 2010, in Blu-ray, CD and DVD formats, and debuted at number 161 on the Billboard 200 and number two on the Billboard DVD charts.
A sequel to "Hangar 18" titled "Return to Hangar" later featured on Megadeth's ninth studio album, The World Needs a Hero.
Credits are adapted from the album's liner notes.
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