Yeah, the story was a little sketchy, if im not mistaken, theyre real purpose was to retrieve the top secret information stored in the city's computer aka the superintendent and bring it back, stopping the Covenant from getting valuable and potentially dangerous information, but while down there, they discovered an engineer aka vergil who had communicated with the AI, and explained that engineers were slaves and that he had valuable information that could help humanity win the war, so the new mission became to get him out of the city safely so he could be debriefed, but you are right to be confused with what the information they got actually did to help anyone in the series, it isnt really explained unfortunately, they dont go into it, i assume it was some general information that would prove useful like battle plans or weaknesses.