If it's the black death, then you can't. It just spreads around. The best way to deal with it is to quarantine the settlement and characters infected and wait for it to pass away. You could also try to keep it going and infect your enemy.
the best thing (the only thing) you can do to "quarantine" a plague is to not move any infected units outside of the settlement until the plague dies down unless you want to do the spy thing mention above. --- You think that Fortune changed in her relation to you; you are wrong. These are always her habits, this is always her nature. -Philosophy