The metro lines are not owned by JR, but JR has their own lines in Tokyo – such as the popular Yamanote loop line taking you to known stations such as Ueno, Shibuya, Shinjuku, Asakusa, Akihabara, Tokyo Station and much more! Having a JR Pass allowing you to use all of it freely. Cities like Tokyo usually need you to combine both a metro train and JR line train to reach your destination as they cover different parts of the city. They do however have stations in many of the same locations, as an example Akihabara Station and JR Akihabara Station.