Assassinating the Emperor is Skyrim. I joined the Dark Brotherhood for the fun, and the achievements, and while I got that, I also killed Tamriel's biggest hope against the Thalmor, and the man I had sworn to serve in the civil war questline.
Legion's loyalty mission in Space Wizards 2: You are given the choice between violating free will at great risk to all involved, (Paragon? Somehow.) and killing a dangerous enemy as you have been doing for the entire mission, with little risk for all parties involved. (Renegade? Somehow.)
Since I was playing Paragon, I did the most evil thing possible, and overwrote the free will of sentient beings to fit my worldview, with the possibility that it wouldn't matter and just get people killed.
Seriously, they totally got the points backwards on that mission.