I'd also like to have seen an explanation of that. She knew they weren't planning on killing T'illips so seems grossly out of character.
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Freeman said she planned to take them to Earth to have them figure out how to keep everyone alive, but my guess is that inside, she was using this to pass the buck to someone else and privately was pessimistic about the chances of figuring out a way to separate them without Janewaying them. That feels like a very Freeman thought process. But yeah, they ought to have said something on screen.
I just assumed that the orchid has some innate "evil" tendency that influenced the personality of the hybrid.
Maybe, but then why didn't Tuvix go evil?