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It is a concept album in which the overarching plot follows the protagonist moving through his own "Downward Spiral", dealing with religion, dehumanization, violence, disease, society, drugs, sex, and finally suicide. Reznor has stated that the character is a representation of himself.
* "Mr. Self Destruct" begins with a sample from the 1971 film THX 1138. It is taken from a scene in which a man is being beaten by a guard depicted on a holographic television. 
* The frantic drumming at the end of "Piggy" played by Reznor himself—his first and only attempt at live drumming on a record, and one of the few "live" drum performances on the album (Stephen Perkins on "I Do Not Want This," Andy Kubiszewski on "The Downward Spiral," and Chris Vrenna on "Hurt"). He states that it was from him testing the mic setup in studio, but he liked the sound too much to not include it. 
* "Closer" uses a heavily modified sample of a kick drum from the song "Nightclubbing" from The Idiot album by Iggy Pop. 
* "A Warm Place" is based on the melody from David Bowie's 1980 single "Crystal Japan." Some hear it as a complete rip-off, while others argue that from a music theory point of view that the structure has significant differences.
* The looping female voice that appears on "Reptile" (approx. 5:06) is from the 1974 film The Texas Chain Saw Massacre. The strange mechanical sound before the drums start can be found in the movie Leviathan and the other sounds during all the song are found in Aliens (the escape in the vessel).
In a three part storyline, an abused and apathetic person (represented by "The Worm") becomes an influential celebrity and finally is transformed into the powerful "Disintegrator". In an issue of Kerrang! magazine edited by Manson, he stated that the album was a tribute to—and inspired by—the philosopher Friedrich Nietzsche. Much of the album content is deliberately vague, allowing listeners to draw independent conclusions.
The album was intended by Bowie to serve as the soundtrack and musical basis for a stage show and/or television production telling the story of Ziggy Stardust. As well as the songs on the album, Bowie also intended songs such as "All the Young Dudes", "Rebel Rebel" and "Rock 'n' Roll With Me" (the latter two later recorded for Diamond Dogs) for this realization of the Ziggy story. In a Rolling Stone interview with William S. Burroughs, Bowie outlined the full plot of the Ziggy Stardust story:
"The time is five years to go before the end of the earth. It has been announced that the world will end because of lack of natural resources. Ziggy is in a position where all the kids have access to things that they thought they wanted. The older people have lost all touch with reality and the kids are left on their own to plunder anything. Ziggy was in a rock-and-roll band and the kids no longer want rock-and-roll. There's no electricity to play it. Ziggy's adviser tells him to collect news and sing it, 'cause there is no news. So Ziggy does this and there is terrible news. 'All the young dudes' is a song about this news. It's no hymn to the youth as people thought. It is completely the opposite. [...]
The end comes when the infinites arrive. They really are a black hole, but I've made them people because it would be very hard to explain a black hole on stage. [...]
Ziggy is advised in a dream by the infinites to write the coming of a Starman, so he writes 'Starman', which is the first news of hope that the people have heard. So they latch onto it immediately...The starmen that he is talking about are called the infinites, and they are black-hole jumpers. Ziggy has been talking about this amazing spaceman who will be coming down to save the earth. They arrive somewhere in Greenwich Village. They don't have a care in the world and are of no possible use to us. They just happened to stumble into our universe by black hole jumping. Their whole life is travelling from universe to universe. In the stage show, one of them resembles Brando, another one is a Black New Yorker. I even have one called Queenie, the Infinite Fox...Now Ziggy starts to believe in all this himself and thinks himself a prophet of the future starmen. He takes himself up to the incredible spiritual heights and is kept alive by his disciples. When the infinites arrive, they take bits of Ziggy to make them real because in their original state they are anti-matter and cannot exist in our world. And they tear him to pieces on stage during the song 'Rock 'n' roll suicide'. As soon as Ziggy dies on stage the infinites take his elements and make themselves visible."
The more generally acknowledged story, however, has Ziggy Stardust himself being the "starman", from Mars, who has come to save the Earth with messages of love and peace, and Bowie has referred to Ziggy as a "Martian" in several interviews.