I don't think it's a GOVERNMENT cover up at all! It's a cover up by a large group that operates outside of any particular government's jurisdiction. Ponder this - to whom is the Dharma Initiative accountable, as far as a country's government is concerned? America - because the DeGroots were from the U.S.? Denmark - because Alvar Hanso is Danish and created the Dharma Initiative? England - because Charles Widmore's labs created the vaccine that was used in Gambia, Africa and (possibly) that the DI used? South Korea - because Paik Heavy Industries built equipment used in the Worldwide Wellness Prevention Development Program in Gambia, Africa and (possibly) that DI used? Governments, for the most part, operate under a system of laws and regulations, national treaties and agreements (I know some of you will argue that, and you know who you are, but for a moment, please, let us assume this). In fact, there is no government responsible for what is happening on the island. It is a sick, twisted multi-national conglomeration of powerful men who are not afraid of any law and have the capital to make anything they want happen.
Also - and some of you have stated this - Desmond was not on flight 815 and, therefore, it doesn't matter to Penny if that flight was not found. Desmond was on a race around the world aboard the Elizabeth - the ship that was given to him by Libby.

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