The Cryptograph, also known as the master key, is an electronic device able to access any computer system including Division's.
Amanda using Anne kidnaps Owen to obtain the location of the cyrptograph. She then uses the cryptograph to infiltrate Division's computer system to deliever a message. The device was recovered from Amanda after a raid lead by Nikita, Alex, Michael and Owen. It appears, however, that Amanda obtaining the device is part of a much bigger scheme surrounding Owen.
After the events of Consequences the Cryptograph was taken to Division HQ.
After using it, Ryan brings the device to the President stating that Division had recovered it and to consider it a token of their value to the country. President Spencer then orders the device to be taken to the NSA.