Muhammad Ali eventually broke open the jar and found a stash of old codices, or leather-bound books. The twelve codices and eight separate leaves that he discovered were not all later classified as Gnostic writings. Some were categorized as philosophical works while others were distinctly Hermetic texts that fit better into the category of Egyptian tales. A total of fifty-two tractates were found.

Muhammad Ali ripped apart some of the books to share with others, but his companions didn't want them. So he removed his turban and used the cloth to transport the books to his home. His mother started a fire with pages from the some of the books.

Muhammad Ali clearly remembered the date of the discovery because he had been involved in a blood feud with a man from a village near the Jabal al-Tārif mountain. His enemy had murdered Muhammad Ali's father, who had been a night watchman, in retaliation for the watchman shooting an intruder. Many months after the death of their father, Muhammad Ali and his brother took revenge. They sought out, killed, and dismembered their father's attacker, according to Gnostic scholar Marvin Meyer, writing in The Gnostic Discoveries. That book states that the brothers cut out the man's heart and immediately devoured it.

At some point after finding the codices, Muhammad Ali gave a few of the texts to a local history teacher. The teacher sent one of the books to an associate in Cairo. He hoped to find out whether or not the codex had monetary value. It did. The later purchase of the texts by antiquities dealers piqued the interest of representatives of the Egyptian government. They acquired one copy and seized ten and a half of the thirteen books. They placed them for safekeeping in the Coptic Museum in Cairo. But someone smuggled out one of the books — the thirteenth codex with five separate texts — and offered it for sale. The codex contained five unique texts but some of the pages were missing. The late religious historian and Gnostic scholar Gilles Quispel in the Netherlands heard about it and convinced the Jung Foundation to buy it. Unfortunately, the manuscript was missing pages. Quispel then went to the Coptic Museum, where he borrowed photos of the appropriate pages and began translating the material. He suddenly realized that he possessed a “secret” Gospel of Thomas, a Gnostic text whose author declared he was Didymos Judas Thomas the twin and that the text contained the “hidden” or secret sayings of Jesus.