Hi,
So I'm currently level 42 and was shocked that the story line just abruptly stopped when I was around 35, after killing the guy who goes bad out of "the five, anyway.... I was wondering what I did wrong and what I can do to fix it
You'll have to finish the Coldharbor zone in order to pick up the very end of the Main Quest. You should get a quest to meet the Alliance leaders at Stirk that starts the Coldharbor zone. Finish that zone and the Prophet will start giving you the final Main Quests.
Those two quests are available once Council of the Five Companions has been completed or once the final quest in the Alliance Storyline has been completed.
That Stirk quest will take you to Coldharbor where you'll pick up the Coldharbor main quest in the Hollow City. Follow the Groundskeepers instructions to get started.
had the same problem but once I figured it out I never went back to coldharbor so now I have 3 level 50's and not one of them has finished the main story.