It took exactly one year for Koch’s high opinion of Baden to sour. Too many unforced errors added up, including picked-apart trial testimony in the “Dr. X” case, leading to the acquittal of Mario Jacsalevich in a spate of poison-murders at Riverdell Hospital; a Housing Authority patrolman whose January 1979 murder went undetected for 12 hours, his body removed from the scene before a proper death investigation; conflicting conclusions relating to the chokehold death of a Brooklyn businessman at the hands of police; and off-the-cuff comments about the possibly sexual-intercourse-interrupting death of Governor Nelson Rockefeller. Not even a high-profile gig as supervising pathologist for the House Select Committee on Assassinations, which looked anew at the JFK and Martin Luther King Jr. cases, could save Baden from the chopping block.

Ultimately, memos from district attorney Robert Morgenthau and city health commissioner Reinaldo Ferrer, documenting their criticism of Baden for “sloppy record keeping, poor judgment, and a lack of cooperation,” were the final straw. (Morgenthau later stated that Baden was “cavalier and uncooperative” with respect to evidence lost by the OCME.) Koch demoted Baden in August 1979, replacing him with Elliott Gross. Vowing to fight so-called political pressure, Baden sued for unlawful termination and was briefly reinstated as chief medical examiner in early 1980. That reinstatement was short-lived, with the lawsuit verdict was overturned by a higher court.