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From Lostpedia

E.E.P is an abbreviation visible on the blast door map. The expansion of the acronym to Emergency Escape Protocol was confirmed in the official Lost jigsaw puzzles.

Clear references on the blast door map:

• "Known to be a hub for E.E.P. conduits" - at 11:00
• "Multiple escape conducts blocked after incident" (indicating the Swan) - at 7:00
• "Possible terminal point for Subterranean E.E.P. tunnel network?" - at 1:00
• "No connection to islandwide E.E.P. network" - at 6:00 (written sideways)

These references suggest that the E.E.P. is a series of subterranean conduits possibly leading to the Arrow. Indeed, the map shows many interconnected tunnels, as does the DHARMA cabling map found by Sayid at the Flame.