RuptureFarms is out of business indefinitely. Molluck can't make any phone call because he's wanted by the Magog Cartel and is awaiting a trial, probably a death sentence. He's in hiding. No other Glukkon is willing to take control of the facility because, although they'd love the power, wealth and fame, they would have to pay a massive fine up front for its destruction. They refuse to take control, so it's Lady Margaret who's facing paying the bill to the Chroniclers.
Originally, Sam was supposed to be held captive in Vykkers Labs, not the ruins of RuptureFarms - they were simply going to appear at the end of the first level of Munch's Oddysee. The Shaman actually says in the game that the ship is stockpiling Labour Eggs to sell to the highest bidder - apparently slave labour is a diminishing force, considering Abe's actions. As for where Sam is actually kept, it's difficult to say. With OWI out of game production, the Munch's Oddysee film could come out first and overwrite the story that the game presents.
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