This may have possible spoilers in it, dont read unless you dont care.
When you play as Resistance, in CCity for example, you are supposed to defend the ‘vaccine’ from security who want to take it for VIP use, when you arm the missile to launch at Founders Tower, it is said there are no people in it, its more of destroying a symbol than killing innocents.
However when you play as Security, you are retrieving a bio-weapon in CCity, and Resistance is firing the missile at a crowded building that will kill thousands.
The question is, are these two different storylines just to make the player not feel like a terrorist dealing with bio-weapons and blowing up towers, or are the two sides just being used, told different things than are really happening, is the ‘vaccine’ really a dirty bomb but the Resistance is fooled by Chen to thinking its a vaccine, do the Founders really want to steal a vaccine for themselves instead of letting Resistance distribute it across the Ark? Personally i like the deceptive idea instead of split stories, it adds more thought to the SP game.