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I got a quwtion though.... if an orginizeation is taken over by the aliens then can you get it back? so that they are not with the aliens anymore?
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No. This mean that you are really in trouble if an important organisation get taken away by the Aliens (such as Transtellar, Marsec, the police force, the governement or the other company which sells you arms).
On the other hand it is often an opportunity to get points and items to sell when you attack those fallen organisations (Like the cult for example, which is usually the first to fall). The trick is not to lose too much soldiers when raiding them. If it is done well and without casualties (personal shields helps a lot) then it is very profitable.
If you become at war with Transtellar you won't be able to use taxis and thus won't be able to recruit personnels. In fact you will be able to recruit them but they won't be able to get to your base so you will never be able to use them. I think you can still recruit Squaddies and to fetch them yourself but the research and engineering personnel will sit in their recrutment spot until they go away by themselves.
Thus having good terms with Transtellar is a must at all time, and if it is taken by the Aliens you're pretty much dead unless you are really at the endgame.