Welcome back to our playthrough of Titanfall's increasingly incomprehensible and irrelevant story!
In episode six, we take to the Boneyard. The Militia have gone into an IMC research facility in the hopes of reverse-engineering a whole load of "wildlife repulsor technology". As far as we can tell, the IMC had a problem with SEGA-esque dragons and developed a bunch of massive repulsor towers to fend them off.
And now the Militia want them...because...erm...reasons. So we have to stop them, because we're the baddies.
At least I'm pretty sure that's what's going on.