Franklin's Alphabet is a cryptic alphabet that was invented by Benjamin Franklin to safeguard enemy secrets, believing that it was superior to the standard 26-Letter Alphabet. During his apprenticeship, Crane had studied Franklin's Alphabet extensively.
When Jenny had recovered Franklin's Notebook while she was tracking supernatural artifacts for August Corbin, she couldn't read what was written on the pages. When she was held captive by Jeremy Crane in This Is War, he read her mind and saw the pages regarding the location of the Gehenna Key, but he was unable to find its location right away since the pages were encrypted. Despite Jeremy having success in decoding the pages, Crane, after reading Franklin's Notebook, was able to locate the Gehenna Key at the clock tower in Sleepy Hollow.
Between Season 2 and Season 3 when Crane went on a walkabout to clear his head on the deaths of Katrina and Jeremy, Abbie had taught herself how to translate Franklin's Alphabet with ease. In Kindred Spirits, Abbie was able to show her prowess in decrypting Franklin's Alphabet by translating the instructions on how to control the The Kindred.
In Season 4, Crane discovered that Agency 355 was filled with texts which are all encoded in Franklin's Alphabet. In In Plain Sight, Crane gave Jake a cipher that can crack the code, which he was able to use to learn everything about the supernatural from the Secret Histories.