The mission labelled "All doors Must Open," the one where you go to talk to an ISC cruiser that wants secrets on your allies. Ring a bell?
Anyway, typically, I get myself a DNH and use it to blast the crap out of the enemy cruiser, beam as many marines as I can over, then book it out of there as fast as I can and rarely manage to take it prisoner. Is there a way to take on the whole fleet that appears on you? Is there some secret strategy I have been missing?