By this time, the James-Younger Gang had ceased to exist with the capture of the Younger brothers during the Northfield, Minnesota raid in 1876. However, Jesse had started a "new" James Gang that continued to rob trains, the last of which occurred on September 7, 1881 near Glendale, Missouri. Shortly after this hold-up, Jesse moved his family to St. Joseph, Missouri where they settled in under Jesse’s assumed name of Tom Howard. With a $10,000 reward over his head, Zee tried to get Jesse to take on a more normal life. And Jesse agreed, right after one last great bank robbery in Platte County, Missouri. It was during the planning of this robbery in a meeting with Charles and Robert "Bob" Ford at Jesse's home, that Jesse would be killed by Bob on April 3, 1882.

Sadly, Zee and her children were in the kitchen when the shooting occurred. At the deafening sound of the gun blast, young Jesse, Jr. ran into the living room to find his father on the floor with blood pouring from his head. Zee then began to scream as little Mary started crying. Though Zee tried desperately to stop the blood, it was too late, her husband was already dead.

Bob Ford was already out the door and Charles spent a few moments trying to tell her how the gun had gone off accidentally. Then, he too, made a quick exit, running after his brother.

In no time, the word spread of the shooting and crowds began to gather around the home talking incessantly about the killing of the notorious outlaw, Jesse James. Young Jesse, Jr., who was only six at the time, didn't even know who "Jesse James" was, believing his father's name was “John Davis Howard” and his own name to be "Tim Howard."

After his death, Jesse was packed on ice and taken by train to Kearney, Missouri where he was displayed and viewed by hundreds of friends, admirers, and curiosity seekers. Later he was buried on the family farm in a plot near the house so that Jesse's mother, Zerelda, could keep an eye out for trespassers or souvenir hunters.