10 Hard Video Game Decisions You Immediately Regretted
4. Destroying The Genophage Research - Mass Effect 2
One of the key plot points in the background of the Mass Effect trilogy is the inhumane bio-weapon used to end the war with the Krogan, the Genophage. The Genophage didn't kill anyone currently alive, but it did heavily cut down the rate of successful births of Krogan infants.
This, frankly, monstrous method of population control is brought to the forefront in Mass Effect 2's companion Mordin Solus, the doctor who created the Genophage. His past comes back to haunt him in his personal mission, as a pupil of his is reported to be experimenting on Krogan women.
In the end, it turns out that these brutal experiments are meant to cure the Genophage...and that he's gotten VERY close. After subduing him, you're faced with a choice, keep the research and have Mordin continue working on it, or destroy it, either to keep the Krogan down or out of disgust at the inhumanity that birthed it.
Even if you destroy the research for the latter reason, and then convince Mordin to start his own research into the cure, you're still left feeling VERY morally murky about your actions. Doesn't help in Mass Effect 3 when Wrex confronts you about it, and says that keeping the research would've had all that horror actually mean something.