The Clemens family returned to the United States believing that Jean could receive proper treatment in New York City.  They sailed on the Minnehaha.

From the New York Herald, October 15, 1900:

I left these shores, at Vancouver, a red-hot imperialist. I wanted the American eagle to go screaming into the Pacific. It seemed tiresome and tame for it to content itself with the Rockies. Why not spread its wings over the Phillippines, I asked myself? And I thought it would be a real good thing to do