-( Story related, cannot be missed )-
When using the time portal to head back to the past, you'll have to conquer the Agorian forces once again. This time, there are a lot more threats. Take them down using any means possible and progressing through the small strip of terrain. Eventually, they will drop down two Hydras for you to take at once. I would suggest standing in front of one, putting that between you and the second, so it can't spit fire at you. Defeat it like you have taken care of Hydras before (before you met Azimuth) and then you will end up progressing (eventually) to face the General of the Agorians.
Just lash out against him using your arsenal. He will put up a shield as his health drops, and you need to remove the fuses to continue the fight. Beyond that, this fight is actually easier than the fights preceding it (the Hydras). At least, they were for me, on Hard.