It's a three or four-part mission about this group of alternate universe Borg that were friendly unlike other Borg. The Borg Queen was I think an Andorian lady and I had to help her and her team of ragtag AU Borg from Prime Universe Borg, and then at the end, there was a choice to either free her from some kind of throne where there's a virus affecting her Borg, or let her do her thing.
Two things I remember distinctly was that there's a Borg cube I could optionally investigate, but get rebuked for it later cause it had tonnes of AU Borg in it. The second was that the entire thing was a hologram that gave "what if" scenarios of what would happen if I chose to free or let the AU Borg Queen do her thing, then the AU Queen told me nicely that I couldn't be trusted with the missions, but she doesn't hold it against me.
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I believe that you are thinking of "Parallel Intersections" and its follow-up "Parallel Intentions", both by @Foxrocks.