On May 24, 1990, Cherney was slightly injured when a pipe bomb exploded in the car he and Judi Bari were traveling in. Bari was severely injured by the explosion. The case was investigated by the Federal Bureau of Investigation (FBI), which accused Bari and Cherney of bombing themselves. Bari and Cherney subsequently sued the FBI and Oakland Police agents for violations of the United States Constitution. Cherney and the late Bari's estate were awarded $4.4 million for violations of the First Amendment (freedom of speech) and the Fourth Amendment (the right to be free from unlawful arrest and illegal search and seizure).
In 2012, he told KHUM radio that he does not consider himself an "extremist," preferring the term "radical." In 2012, Cherney's documentary film Who Bombed Judi Bari? was released. There is an ongoing lawsuit against the FBI to prevent it from destroying evidence that could contain the bomber's DNA, and Cherney indicated in a Democracy Now interview that he believes the FBI was guilty of not only framing him and Judi but of a cover-up. Cherney has stated elsewhere that “I believe the bomber is findable.” In October 2012, Cherney announced a $50,000 reward “for information leading to the identification, arrest, prosecution and incarceration of the person or persons responsible for the attempted assassination of Judi Bari by placing a bomb under the seat of her car.”