Whats in a box mission

I didnt get what went on? Independent haven mission, went to get a neural transplant for the haven leader, got to the site and there qas a bunch if new jericho and pandorians fighting

Why were the new jericho guys there? If it was their home(which it wasnt) why wouldnt they be fighting me too? There were more new jericho units than pandorians making it one of the easiest battles. Also i couldnt control the new jericho guys

I just… dont understand what went on?

Go to the independent haven that gave you this mission and then you get the answer, mostly, because it depends on what you answer to them.
You can make a save before you arrive, then you maybe get the whole story (I never did it and choose always the same, so …).