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- The secondary protocol gives explicit instructions into how to move the Island. After reading them Keamy knew what to do to catch Ben, as the secondary protocol would explain the criteria for its use, and how to carry it out. Keamy was basically using the secondary protocol book to work against the secondary protocol Ben was trying to carry out. Some evidence of this is the fact that the protocol has the Orchid on the cover. The fact Ben was trying to use the Orchid to carry out a task, while Keamy only ended up trying to set an ambush up at the Orchid gives a suggestion who was following the protocol and who was just using it to get intelligence on how to stop it.
- Daniel knows about the Secondary Protocol because he's been to The Orchid before (through his time travelling, and as evidenced in his diaries).
- Daniel has been/will be in the Orchid station, as shown in the Season 5 opener.
- The Secondary Protocol involves using the H-bomb that Daniel asked to be buried in concrete in Jughead. Charles Widmore is well aware of this bomb, as it was a major issue at the time, and it is quite possible Widmore also knows where this bomb was buried.
- He'd know that Jughead kaboomed in the 70s.
- The Secondary Protocol is information on destroying the Island. The DHARMA Initiative couldn't figure out how to work the FDW, but they realized it connected to the primary energy pocket on the island, bigger than the Swan's, even. Blowing up the FDW would detonate the Heart of the Island, and destroy it. Secondary Protocol would be implemented in case the Hostiles tried to make them leave the Island. Widmore ordered the Purge when he learned of Secondary Protocol's existence (presumably from Ben, though given he was just a workman, that's iffy), and took it. He gave it to Keamy under instructions to only use it if Ben called in Smokey for backup or something otherwise catastrophic.