Guild Wars 2

Was just wondering, to make sure, if I join a friends story and tag along, am I not supposed to get end mission exp and karma?

It depends. Did you make the same story selections as they did? Meaning if they are on a story part that you are also on normally…. at the end of it you will get progress on the story as well. If their story path is different from your and you are just helping him, then your rewards are the xp and loot you get while helping them kill mobs.