Dr. Bulkeley used hot onion poultices to treat the fever. His method was revolutionary at the time, and was successful in saving Mercy's life.
Common medical practice back in 1687, when the story takes place, was to treat fever by bleeding patients. It was believed that by doing so, poisons infecting the body and causing the illness could be eliminated. It has since been discovered that bleeding did more harm in most cases than good, serving mainly to weaken victims even more, and compromising their chances of overcoming the fever by virtue of their own natural defenses. When Mercy fell ill, "the young doctor rode out from Hartford to bleed her," but after trying twice, he decided helplessly that he "dare not bleed her further." The method did not help Mercy, but only seemed to weaken her, and she was very near death.
It is not stated specifically what kind of fever Mercy had, but it is evident that the primary danger to her life was caused by the extreme congestion in her lungs. Operating on a theory on which he had been reading, Dr. Bulkeley instructed the family to slice onions and boil them to just the right consistency, after which he "piled them in a mass on a linen napkin and applied the blistering poultice to Mercy's chest," repeating the process over and over until there was evidence of improvement in her condition. Although he may or may not have been able to explain exactly why his method should work, Dr. Bulkeley was indeed on the right track. The poultices relieved the congestion in Mercy's lungs, enabling her to breathe. Thus relieved, her body was then able to overcome the fever, and Mercy eventually recovered (Chapter 17).