Enemies are going to happen to pretty much everybody at some point or another. That's why you got points for them.
There are possible negative reprecussions for unit members if you work for
or conduct operations inside any of the following Successor States:
Capellan Confederation
Lyran Commonwealth/FedCom
Federated Suns/FedCom
Draconis Combine
Free Rasalhague Republic
St. Ives Compact
Essentially, pretty much all of them.
Desire for CC contract increasing. Rob, can enemies be bled out/eliminated?
You have to both do "story" stuff AND spend XP on it. As per the RPG rules, buying off negative traits is hugely expensive, which is why I didn't even bother putting in XP costs for them. As per the MW3rd edition to ATOW playtest conversion document (internal CGL document, sorry), a Trait Point in MW3rd is worth ~35 XP, or roughly the cost of raising a mid-range attribute by 1 point. So an Enemy(2) Trait costs ~70 XP to buy off, PLUS you have to justify it via actions achieved in-game.