Fergus Fraser died in a blaze that tore through the family print shop in the episode titled "Evidence of Things Not Seen," ending a run that had started in Season 2. The fire broke out later the same night after anonymous threats were wedged into the family's front door and Marsali had been hit with a tomato while shopping with Brianna.
Earlier in the episode, Fergus had been teaching Germain and Henri-Christian how to work the machinery at the printshop, repeating the conviction that the pen is their sword and that they can never lay it down. That choice became fatal when the Fraser family's shop caught fire and Marsali got the girls out of the house as the flames spread. Fergus climbed to the roof where the boys had been looking at the stars, and they were lowered over the side with a pulley system, but Henri-Christian cried that he was slipping and fell in the rescue sequence before Roger caught him and saved him.
The roof underneath Fergus then gave way and he plunged into the inferno. Jamie startled awake in bed and told Claire, "I dinna ken, but I have a terrible feeling something's wrong," while the fire still burned elsewhere. The loss lands hard because the print shop and Fergus's political side-taking had already drawn hostility from townsfolk, and the episode's turn is described as a huge diversion from Diana Gabaldon's novels. It also gives a definitive answer on whether Faith lived, closing off one thread even as another is torn open.
That grief is sharpened by a later exchange at Lord John's, where Brianna asked Roger whether he would stay in the past if she died. Roger said he would stay because "Our whole family's here," and Brianna answered, "Five," correcting the count of four and pointing to the child they are already carrying in the family's future. Marsali then put words to the marriage that had been built around Fergus's stubbornness and work, saying, "After all these years, I dinna ken where he ended and I began." Brianna told her that Fergus lives on in their sons and daughters. The episode leaves no ambiguity about the cost of the fire: Fergus is gone, and the family will have to carry both his loss and the life he built with it.