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Was the Son literally inside of the Father so that they were one? Was the Father and His body inside the Son? Of course not—They were separated by how millions of miles of distance between where the Son was on earth and where the Father was in heaven. They were in union with one another in mind, in will, in purpose.
What were They doing? They were joined together in the accomplishment of the same purpose, and now Jesus prays that we might be one with Them in the accomplishment of the same purpose, having the same will, the same mind, the same character, the same hopes, the same goals, the same end in life.
John W. Ritenbaugh
Image and Likeness of God (Part 4)