The Manuscript was a Kryptonian map that was originally found in China by the Duchess Gertrude of Castelnois de Montmiral, France, and was later stolen and hidden by her rival, the witch Countess Margaret Isobel Thoreaux, in 1604. It contained information about the location of one of the Stones of Power, the Crystal of Air, in Shanghai. The map translates Tree, Mountains, Ruins, Badlands, and Plains. It turns out that it really was not a map, but a drawing of a tree, mountains, and ruins.
Lex Luthor purchased this document from a private collector in St. Petersburg. According to Lex, the history of that Manuscript page, is that it is the last surviving page from a 14th Century manuscript. It depicted the Grand Prince Donskoi's victory over his mortal enemy Mamai at the Battle of Kulikovo. Legend has it that this was the only object adorning the walls of Rasputin's chamber while he studied at the Verkhoturye Monastery. He believed this page would reveal a path to unimaginable power. Rasputin would stare at it for days at a time attempting to penetrate its secrets.Clark Kent recognized the border design of the manuscript as Kryptonian symbols as spelling out the message "Look deeper." When he used his x-ray vision, he saw a map hidden beneath the image. Bart Allen stole the map in an attempt to sell it for profit, but due to Clark's influence, returned it and turned over a new leaf. A day or so later, Clark came by to check up on the aftermath of Bart and the Manuscript, finding things were back to normal for Lex. As Clark was departing the Luthor Mansion, Lex was looking at the map inside the Manuscript himself, with his laptop.
Later, the witch Countess Margaret Isobel Thoreaux, possessing the body of Lana Lang, saw the artifact in the Luthor Mansion and knew that Lex was also seeking the Stones of Power. When Lionel gave Jason Teague a copy of the map, he secretly left for China. Lex quickly showed up in China with Jason and they both were captured and thrown in prison while searching for the Stone of Air. Later, Lana also showed up in China, having taken the map from the possession of Lionel.
Once Lana was found, captured and tortured in prison herself, she became possessed by Isobel once again. The Stone of Air was only discovered when Isobel broke free from the prison and found the tree illustrated in the "map" herself, buried underground and inside a fragile horse statue.