- "It was written in an exotic language I did not recognize and full of drawings. Plants and animals out of an opium dream."
- ―Le Chasseur describing the manuscript, 1752.[src]
Commonly, though erroneously, believed to have been written circa 1405, the artifact was created long before. Previously in the possession of Emperor Rudolf II of the Holy Roman Empire, four of the manuscript's pages eventually wound up in the hands of Governor Peter Beckford of Jamaica by the early 18th century. After they were taken from the Beckford estate, the pages were scattered across the Caribbean, until they were eventually collected by the pirate-turned-Assassin Edward Kenway between 1715 and 1722.
In the following decades, the Assassins and Templars alike learned of the connection between the manuscript and the mysterious Precursor box, one of the only devices that could translate its incomprehensible text. In 1755, the inventor Benjamin Franklin was the first known human to properly use both pieces in tandem, electrifying the box with lightning. It was during this experiment that the Assassin Shay Cormac discovered the location of a hidden First Civilization Temple hidden underneath the Carmo Convent in Lisbon, Portugal.
After Shay returned to the Davenport Homestead, he stole the manuscript from Achilles Davenport's manor in an attempt to stop the Assassins from discovering another First Civilization Temple and causing another earthquake. Though Shay almost managed to escape the Homestead, he was shot by the Assassin Louis-Joseph Gaultier, and fell from a cliff. Some time later, the Templar George Monro found Shay and the manuscript. Rescuing Shay and keeping him in the care of Barry and Cassidy Finnegan, Monro took the manuscript for himself.
In 1757, Colonel Monro trusted Shay, now a Templar ally, with the manuscript, giving him the mission of discovering its secrets. Later that year, during an attack on Albany, Shay attempted to save Monro from the Assassin Kesegowaase and his native allies. Once he accomplished his mission, Shay gave Monro the manuscript and sent him to the Morrigan, while he stayed at Fort Frederick and battled Kesegowaase. When Shay managed to kill him, Kesegowaase revealed with his last words that the Assassin Liam O'Brien had already killed Monro and stolen the manuscript.
In 1759, the Assassins were making the preparations to make an excursion to another Precursor Temple, while Hope Jensen and Liam replicated the experiment Benjamin Franklin had made years ago. By doing so, the Assassins discovered that another Temple was located in the Arctic. After a lengthy chase through the structure, Liam was killed and Shay took back the manuscript for the Templar Order.
In 1839, the Mentor of the Indian Assassins, Hamid, tasked Arbaaz Mir with the recovery of a map from the Voynich manuscript detailing information on the Koh-i-Noor diamond, during their quest to protect the artifact from falling into the British Templars' hands.
In 2013, Abstergo Industries warned memory research analysts at Abstergo Entertainment, who were assigned to relive the memories of European subjects during the 15th and 16th centuries, to look out for the Voynich manuscript during their Animus sessions, especially for its supposed connection to the English philosopher Roger Bacon.
- The manuscript is named after book dealer Wilfrid Voynich, who purchased it in 1912.
- It is theorized that the Voynich manuscript may have been sold to Rudolf II by John Dee. Another theory suggests that the manuscript was written by Edward Kelley, who could speak with members of the First Civilization through his Crystal Ball.
- The map Arbaaz acquired features the Voynich manuscript pages Folio 70r and 75r, as well as drawings of the Koh-i-Noor, two Apples of Eden, a Memory Seal and symbols found on Marcus Junius Brutus' drawing of the Colosseum Vault.