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"Obelisk The Progenitor", known in the Japanese version as "True Ancestor Obelisk" (真祖・オベリスク, Shinso Oberisuku), was used by Yugi in chapter 42 of the Yu-Gi-Oh! R series when he played the spell card "Divine Evolution" (belonging to Gekko Tenma) on "Obelisk the Tormentor" (known as "God of the Obelisk" in the manga).
"Obelisk the Progenitor" seems to be no different from "God of the Obelisk", except for its appearance, which is that of the Ancient Egyptian Version of "God of the Obelisk" seen in Yu-Gi-Oh! Millennium World. It appeared briefly and was mutually destroyed with "The Wicked Avatar". The mutual destruction occurred because "Divine Evolution" had increased "Obelisk's" rank in the Divine Hierarchy, a manga-only concept which means that if God cards with equal attack attacked each other, ones of higher rank ("The Winged Dragon of Ra" and "The Wicked Avatar") would destroy those with rank below them.
"Obelisk The Progenitor" seems to look like the original art for "Obelisk the Tormentor" drawn by Kazuki Takahashi which would be later used on the legal version of the card.