An important quote from the dissent (complete text is here):
Construing the Commerce Clause to permit Congress to regulate individuals precisely because they are doing nothing would open a new and potentially vast domain to congressional authority. Con- gress already possesses expansive power to regulate what people do. Upholding the Affordable Care Act under the Commerce Clause would give Congress the same license to regulate what people do not do. The Framers knew the difference between doing something and doing nothing. They gave Congress the power to regulate commerce, not to compel it. Ignoring that distinction would undermine the prin- ciple that the Federal Government is a government of limited and enumerated powers. The individual mandate thus cannot be sus- tained under Congress’s power to “regulate Commerce.” Pp. 16–27.