There's really only two possibilities if Misaki is getting shot at by the Exoskeleton guy.

a) She's working to complete Kimijima's master plan, whether that be good or evil.
b) She's working to stop Kimijima's master plan, whether that be good or evil.

It's really hard to figure out who the bad guys are here. I'm pretty sure the Exoskeleton guy is working for the Council of Ultra Evil. What isn't clear is what side Kimijima was on, and which side Misaki is on.

If she was asking about the rocket launch though...I would say that she is trying to stop the pending apocalypse.

Argrh! I'm so confused about who to hate!


But what I really enjoy about this series is the interludes of:
Akiho's Adventures in Building Robots While She Isn't Very Good at It.

Kai has been keeping her out of the whole conspiracy thing, so she gets to live her life, trying to fulfill her good-hearted dreams. In this episode, it finally paid off. Even if the general populace hates Gunvarrel, Ahiko got one little boy to love it again and tell her it was cool.