In the first settlement done at Gilgal in the book of Joshua, what happened to the tribe of Joseph?
The tribe of Joseph was the one tribe that was further broken down into two parts. Joseph's two sons, Manasseh and Ephraim, were each recognized as the head of a separate tribe, dating back to the time of the Exodus. (Num. 1:10) When the census was taken of the people being led by Moses, as first listed in Numbers chapter 1, the descendants of Joseph were counted as two tribes.
Of the people of Joseph, namely, of the people of Ephraim, their generations,...every man able to go forth to war: the number of the tribe of Ephraim was forty thousand five hundred. Of the people of Manasseh, their generations,...every man able to go forth to war: the number of the tribe of Manasseh was thirty-two thousand two hundred. (Num. 1:32-35)
When the twelve tribes of Judah crossed the Jordan River and took possession of the Promised Land, the tribe of Ephraim and the tribe of Manasseh were each given a separate assigned territory, as determined by the drawing of lots. The two tribes were given territories shared the brook Kanah as a boundary.
Then the boundary went down to the brook Kanah... Then the boundary of Manasseh goes on the north side of the brook and ends at the sea; the land to the south being Ephraim's and that to the north being Manasseh's (Josh. 17:9-10)