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Odyssey Protocol is a S.H.I.E.L.D. protocol used for the emergency evacuation of a team from one of its facilities.
Agent Phil Coulson, the highest ranking S.H.I.E.L.D. officer in the Hub during the HYDRA Uprising, was contacted by United States Air Force Colonel Glenn Talbot. Talbot informed Coulson that his troops would be arriving shortly to take control of the facility.
Knowing that Talbot viewed S.H.I.E.L.D. as a terrorist organization and would arrest all agents he found, Coulson enacted Odyssey Protocol and ordered Skye to erase all online proof of his team's existence before fleeing the Hub on the Bus.