He lived for a year in a housing cooperative in Chicago, and later became associated with the Arab-Jewish Peace Alliance in Albuquerque, New Mexico, where he came into contact with the ISM. Shortly thereafter, in January 2003, he traveled to the West Bank to participate in ISM protests against Israel.

Avery appeared before the Israeli Supreme Court on February 28, 2005 to request a Criminal investigation into his shooting. He accused Israeli troops of shooting him without provocation. The court responded by ordering the military to reopen Avery's case. Avery's attorney, Michael Sfard, said that the ruling "shows the military that even internal inquiries should be managed professionally and with care to get testimony from all sides, not just from military," and that it "coerces the military to change its stand on things. This is definitely not usual."

In November 2008, Avery accepted a settlement for NIS 600,000 (USD $150,000) from the state of Israel in exchange for dropping the lawsuit. According to Shlomo Lecker, his Israeli Lawyer, "The sum does not reflect the injuries Avery suffered... On the other hand, it's one of the very few times the state has awarded damages to anyone hurt by the IDF during the Second Intifada." Lecker said that Avery was willing to settle because of the need to defray some of the costs of the reconstructive operations he must still undergo, in addition to skepticism that the 15-month-long investigation would ever reach a satisfactory conclusion.

According to the Jerusalem Post (9/20/07; 11/19/08), Brian and his associates were "wearing red reflector vests with the word "doctor" in English and Arabic." The army refused to order a formal investigation of the incident, since that their probe found that no Soldiers on patrol in the area that night reported such an incident as it was described by the four witnesses.