With my changes for the campaign AIs, the story will feel more as it is supposed to, in my opinion ;) This is no real mod for FA, you only need to replace files of your FA installation. Easy installation and lots of fun changes ^^
Quick fix for the second mission! To be precise, you now CAN complete the mission so you can enjoy the battle of the massive bases :)
This doesn't only fix the bug not moving on to the last phase, it also includes some small changes in platoon types and the size, as well as adding 3 Corona Air Superiority Fighters to the Order forward base during the first phase. Having them really decimates Loyalist airforces, which could have made it easier for you in the beginning.
Have fun ;D