[1] After receiving a National Security Letter (NSL) from the FBI, he sued the FBI and Department of Justice and became the plaintiff in the lawsuit Doe v. Ashcroft (filed April 9, 2004 in the United States) filed on behalf of a formerly unknown ISP owner by the American Civil Liberties Union and the New York Civil Liberties Union against the U.S. federal government.

The letter—on FBI letterhead—requested that Merrill provide 16 categories of "electronic communication transactional records," including e-mail address, account number and billing information.

[3][4] Because National Security Letters are accompanied by an open-ended, lifelong gag order, Merrill was unable to be identified in court papers as the plaintiff in the case and instead was referred to as "John Doe".

In fact, in 2007 The Washington Post made an exception to its policy against anonymous op-eds to publish an editorial by Merrill because of the gag order.

The first was a September 2004 district court decision that the national security letter statute was unconstitutional, which prompted Congress to amend the law to allow a recipient to challenge the demand for records and the gag order.