Discharge (Purple Sky)

So i just rewatched the season 2 finale and what was the deal with the sky turning purple and the two scientists in the end?

Also in "Not in Portland" Jack asks Tom why they didn't just take Ben to a real hospital in the real world if they have access to a ship? Tom says "We would, but ever since the sky turned purple..." he then ended midsentence since Ben was bleeding.

Has this been answered yet? did the writers say they were going to direct this in the last season? any understanding or help would be great!


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