From Future's End Wiki
Choosing a Faction It is important to remember that neither faction within Future's End is considered 'good' nor 'evil', though individuals’ perceptions may view them as such! Each faction is inherently good, but with different ideologies and methods which mean that working closely together is all but impossible. It is also important to note that while Alpha is not sanctioned by the UEG in the same way that Omega is, they are still tolerated globally due to the fact that they are an effective force for good. Being part of Alpha does not brand you as a criminal.