The band started working on a full album, titled Sub, at London's Trident Studios in 1998, with renowned producer Roli Mosimann (Björk, Marilyn Manson, Faith No More), who had also produced the 1990 Celtic Frost album Vanity/Nemesis. Further recording and mixing sessions took place at EastSide Sound in Manhattan, Nomis Studios in London, and at various studio locations in Switzerland. Sub features prominent final mixes by Mosimann, John Fryer (HIM, Nine Inch Nails), and Apollyon Sun themselves. Sub was released globally through Mayan Records in late summer 2000, after two years of studio work.

"Human III" is the continuation of a song developed by Tom Gabriel Fischer, following on from "Human (Intro)" from Celtic Frost's Morbid Tales (1984) and "Human II" from Celtic Frost's Cold Lake (1988). "Messiah (Second Coming)" is a remake of the Hellhammer song "Messiah", Hellhammer being one of Fischer's former bands. "Reefer Boy" and "Concrete Satan" both appeared on the God Leaves (And Dies) EP, however they were completely re-recorded for Sub. There are several unreleased songs from these sessions including "Cradle", a re-recorded version of "God Leaves" and two further instrumentals.

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