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It was significant to the conspiracy because of its effects on alien physiology and spacecraft. New Mexico was known to have vast sources of magnetite. When a UFO flew overhead in 1947, the magnetite caused the ship to crash. (TXF: "The Truth")
In 2002, Dana Scully learned that magnetite was the only means of killing a supersoldier. While pursued by the Shadow Man, who wanted to use her in his plan to kill Fox Mulder, Scully became isolated from Agents Doggett and Reyes in a mine. Having been cornered, Scully was unable to defend herself from the supersoldier. However, the mine contained a vein of magnetite. The Shadow Man was dramatically affected by it, his skin turning gray and his body literally disintegrating before being pulled with tremendous force straight into the rock, obliterating his body. (TXF: "Trust No 1")
While Mulder was on trial after supposedly killing Knowle Rohrer at Mount Weather, he mentioned the magnetite vulnerability to the other agents, who confirmed it based on the incident with Scully. With help from Alvin Kersh, Mulder was spirited away with Scully and told to leave the country. However, he traveled to New Mexico, where the Cigarette Smoking Man had been living for two years. The CSM also knew of the magnetite vulnerability and lived in a pueblo surrounded by it to keep supersoldiers away. The conspirators, however, followed. Doggett and Reyes raced to save Mulder and were confronted by Rohrer. Rohrer must not have been aware of the magnetite in the nearby hills and was destroyed by it. (TXF: "The Truth")