The JackBNimble program was bequeathed to Captain Chaos by Dunkelzahn when he died, and the Captain never managed to break the encryption on the file. In 2065, the assault of the Jormungand worm shredded the encryption on the file and caused it to activate, "saving" Captain Chaos and others who were dying in the Matrix. The current whereabouts of JackBNimble are unknown.
To Captain Chaos, I leave the encrypted file JackBNimble. Whatever rewards it reveals are yours. I had no success trying to decrypt this thing, but I've always believed it contained some communication from another world. Of course, I could be wrong. I've also notified the Draco Foundation to provide for your well-being in the event the file deals you a debilitating injury.
As a program, JackBNimble has no physical representation. In the Matrix, it has only been seen as a shadow. The JackBNimble program appears to be at least as complicated as a semi-autonomous knowbot, and appears to be able to "save" deckers as files - which, under certain circumstances, can appear to "wake up."