How was the agent of the other research facility saved?
That's a good question, I like it. 
Spoilers up to the last chapter of the manga below. 

Here is what the Agent says in the last chapter:


   


I suppose what really saved her was 


   the Vector Attack Craft, the same one that save Arakawa on the shore. The Vector Attack Craft was developed in Saseba - a research project of the government, basically ruled by the same people that were the Agent's bosses. So the guys in the Vector Attack Craft had some kind of motivation to save the Agent.