Because JSTOR computers were in another state, thus the federal involvement. Which still doesn't answer the question of why the CFAA related charges as I'm fairly certain JSTOR systems are not part of a govt. agency. Unfortunately once the federal system get's their eye on you and assigns monetary damages in excess of five figures they don't let go. I would assume MA computer fraud law would be more understanding considering the reputation of MIT. Otherwise a majority of engineering students would find themselves facing Ortiz & Heymann.
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