The Pentagon named Ellis to be the NSA's top lawyer, starting a day before President Biden's inauguration on Jan. 19, but the new administration immediately placed him on administrative leave and opened a security inquiry on Jan. 20.
"It has been an honor to protect my country as a national security professional since 2007, and I remain ready to serve as General Counsel of NSA," Ellis wrote in his letter Friday. "However, I have been on administrative leave for nearly three months without any explanation or updates, and there is no sign that NSA will attempt to resolve the issue. I therefore resign my position, effective immediately."
A biography page for Ellis on the NSA's website is still labeled as "pending."
"What happened to Michael Ellis reeks of political payback, and Intelligence Committee Republicans will be closely examining all these events," Rep. Devin Nunes, R-Calif, told Fox News in a statement. Nunes is the top Republican on the committee.
Ellis, who previously served as an attorney for the National Security Council and the White House’s senior director for intelligence under former President Trump, was placed on leave due to a pending Department of Defense (DOD) Inspector General (IG) evaluation and an NSA security inquiry into the handling of classified information.
Sens. Chuck Grassley, R-Iowa, Joni Ernst, R-Iowa, and Tom Cotton, R-Ark., previously demanded an inspector general's investigation into Ellis being placed on leave.
"The Biden administration’s decision to place Ellis on leave appears to be politically motivated and we request that you begin a review of the facts, circumstances and process that the administration used to justify their decision to place him on administrative leave," the senators wrote in a March 8 letter to Defense Department Acting Inspector Sean General O’Donnell.
Democrats were vocal in rejecting Ellis' appointment to NSA general counsel earlier this year, calling him a "Trump loyalist."
House Speaker Nancy Pelosi, for example, called on acting Department of Defense Secretary Christopher C. Miller to "immediately cease" plans to install Ellis as the new general counsel just days before Biden was inaugurated, describing the decision as "highly suspect" and a threat to the national security of the country.
In a Jan. 17 letter addressed to acting Department of Defense Secretary Christopher C. Miller, Pelosi also called for an investigation into alleged "irregularities" in the NSA General Counsel selection process, arguing that Ellis, "a relatively recent law school graduate with a limited resume, was selected due to interference by the White House, and was chosen over much more qualified candidates."
In a March 23 letter, Ellis expressed disappointment with Nakasone's immediate decision to place him on leave and declared that he was willing to "resolve any concerns" the NSA director may have had.
Ellis details a rigorous application and interview process and eight years of work experience qualifying him for the position he was appointed to in January. He also says no one has come forward with any allegations of inappropriate behavior or an improper, political selection procedure.
"Any DOD evaluation of the selection process does not involve my Conduct, and there is no reason that an evaluation of the conduct of others should preclude me from carrying out the duties of General Counsel of NSA," he wrote at the time.
He added that no one has ever asked him to perform duties "as General Counsel of NSA based on politics."
"If anyone had made such a request, I would have rejected it," he wrote. "...I have never imagined that my political views would have any bearing on how I would do my job as a nonpartisan intelligence professional."
Ellis is not the only NSA general counsel to have ties to former administrations. Glenn Gerstell, who served from 2015 to 2020, raised $50,000 for the Obama campaign in 2012, according to The Washington Post. His predecessor, Raj De, previously served as Obama’s White House staff secretary.
Fox News' Danielle Wallace contributed to this report.