Basically, there comes the choice of whether to activate the RSI, potentially curing all people in the world of the disease (which conduits are immune to) but also killing all current conduits, or joining the Beast to help in awakening the conduit gene in the populace, curing the plague in those individuals, but killing the rest.
Now I chose the latter, because in my mind, the conduits are the superior people. In choosing the 'good' ending, you're essentially halting humanity's evolution, at least for the foreseeable future. It feels wrong just to kill off the stronger beings just to keep the inferior populace in the status quo.
I should point out that I'm a Magneto supporter, in case that wasn't already apparent.