Martin Keamy retrieved the file containing the secondary protocol from inside a safe hidden in a filing cabinet in the captain's stateroom aboard the freighter. The safe required two keys to open; one key was possessed by Keamy and the other by Captain Gault. Keamy took Gault's key by force before opening the safe. Gault claimed that he and Keamy were supposed to open the safe together. Although the content of the Secondary Protocol was never seen nor mentioned, it addressed the Orchid, as Keamy seemed to know where to go immediately after reading the protocol. ("Cabin Fever")
The secondary protocol was secured with a technique known as the ""Two-man rule"." This is a control mechanism that is supposed to ensure safety, security, and/or control over something significantly dangerous and/or valuable. The implementation of the two-man rule in this case was exceptionally poor.