Just posting this in case someone else comes across similar issue:

I came back to Covenant and Jacob was acting like he really had something to say, but apparently the audio file was missing or glitching out. He was trying to initiate this 'Defend Covenant' Quest, and continued to have some interesting dialogue issues. If you're having a similar issue you might want to watch to see how I progressed through it.

https://www.youtube.com/watch?v=xb3bvKpECOI