The secondary protocol is a set of DHARMA Initiative operational instructions obtained by Charles Widmore that was used by the the Kahana's mercenary team. The protocol contained information that the mercenaries were able to use to discover the location of Benjamin Linus following the mercenary team's failed assault on the Barracks. ("The Shape of Things to Come")
On the Kahana
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")
On the Island
When Daniel Faraday overheard that Keamy was heading to the Orchid station, he became concerned and told Charlotte that Keamy was operating by the secondary protocol and that they would have to get off the Island. ("There's No Place Like Home, Part 1")
- 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.
- The Two-man rule is used to enforce a key security concept known as separation of duties.
- For fan theories about these unanswered questions, see: Secondary protocol/Theories
- What did the secondary protocol contain?