The mission to kill NSF leader Juan Lebedev aboard his 747 in one of the early Deus Ex stages seems like a straightforward part of your job as an up-and-coming UNATCO goon: Get on the plane, waste the guy, head home for celebratory drinks. And for a lot of players, that's exactly how it went. JC Denton is a cutting-edge killing machine, after all.
But Deus Ex is a chatty sort of shooter, and so even though I didn't have the non-lethal options that were on the table in your first missions, I had a chance to converse with my target a little bit before I pulled the trigger. Eventually, though, my hard-ass boss Anna Navarre busted in, really pissed off, and demanded that I quit goofing around and do my job. She also warned, helpfully, that if I didn't, she would. One way or another, Juan was going down.
That's how it seems bound to play out, anyway. But it's not. It isn't immediately apparent (or at least, I don't recall it as such), but you can opt to protect Lebedev and take out Navarre instead. The infamous Flatlander Woman is a seriously tough opponent, but I managed to pull it off, and suddenly found myself in a completely unexpected situation: My supervising agent was dead, the guy I was meant to kill was very much not dead, and everything leading up to that point, including my budding career, was now completely off the rails.