(Spoilers) Im on Chapter 4 and sorta have a idea whats going on but I really dont know. I know Hale is dyeing and needs medicine every so often and that we are fight but why im going to random towns and now genesis base? I just need some help its hard to follow. 

Yea, I don't see the story either. Its no toward the ending where the game finally shows some light on the story on what and where. All I know is that Hale is dying and rejects his medicine and all i know is going to these random towns to help fight the aliens away from us. Basically just fighting them to back off and make them weaker and slow them in conquering us. 

R2's story mainly consists of:
"OMG HALE, WE NEED TO GET YOU FIXED UP OR YOU WILL BECOME TEH CHIMERAAA!!!11"
"SCREW YOU, I'M HARDCORE!!!111 BRB GONNA DESTROY MOAR TOWERS AND BATTLESHIPS LOLOLOLOL"

So basically, Hale doesn't want to screw around because he may or may not die. He wants to make his last hours count. I just beat it today, and everything ends in an "OH SNAP".

Not the best story, but damn, those bosses were pretty cool.