@Cody Hill It will probably end much like the original cold war did. There isn't really a bad guy to defeat since the end goal is peace anyway. If there is going to be a bad guy I would like it to be the organization who experimented on Anya.
@Ronin They'll definitely play a big part in the end game of the series it's likely how they'll find out about Anya's abilities. The ending will obviously be Loid being assigned to protect Anya to make sure no one ever gets their hands on her powers.