Deus Ex did a good job of this. I know you were supposed to sympathise with the NSF terrorists, but at the start of the game they're just that - terrorists. It's only when you actually look at what they do and talk to them that you realise you're fighting for the wrong team. The NSF use tranquilisers, UNATCO uses rifles. The NSF doesn't go out of their way to clear out UNATCO forces, whereas they are the opposite. You chat with the terrorist leaders, you talk to the troopers in the interrogation rooms and you realise what they're actually fighting for is a fairer world for everybody, not just the fatcats.
Again, we all know by now that you're meant to view them under a better light than everyone else has you believe, but it was still executed rather well and the whole twist regarding your brother didn't feel heavy-handed at all because of it, and as a result, it did not feel forced when i'm suddenly fighting for the NSF.
Again, we all know by now that you're meant to view them under a better light than everyone else has you believe, but it was still executed rather well and the whole twist regarding your brother didn't feel heavy-handed at all because of it, and as a result, it did not feel forced when i'm suddenly fighting for the NSF.