Chun was allegedly promised a tenure-track position with the department when he accepted. His duties matched or exceeded the senior professors of the department. Chun brought in $1.4 million in research grants, had 26 research publications in international journals, represented Canada at a United Nations conference, supervising graduate students, and teaching classes.
As a research associate, he was not on the university's payroll. He depended upon research grants to fund his work and cover his living expenses as well. Chun remained a research associate for ten years, while being passed over for tenure four times. One time, when he applied, the other candidates were given a month to prepare for the presentation, while he was only given a few days. In another instance, Chris Chapman was selected over him but only stayed for a short time before leaving for the private sector, while the position was eliminated after his departure, leading to allegations that Chapman was given the job in order to preempt Chun from getting it. Up to 1992, as Full Member of the Graduate Faculty, Chun held the responsibilities of a professor, as he supervised graduate students and taught lectures, but not the pay and benefits that accompany such a position.
In 1994, Chun complained to the Dean of Arts & Sciences, stating that he would commit suicide if the search process continued to be unfair, and his suicide threat would later be frequently used against him. The campus police were called in to shut down Chun's lab and escort him off the premises, telling him not to return.
The University however refused to acknowledge the AF&T report and its recommendations, and tried to have the OHRC dismiss the case. The case dragged on for years. Back in 1994, the University's own appointed investigator for the case, Dr. Cecil Yip, stated that Dr. Chun "...acted and has been treated like a professoriate in spite of the fact he has derived his salary support entirely from his own external research contracts. And he has served the Department and the University well in this capacity." Further, "...it is certainly justified for Dr. Chun to feel...he is being penalized for good performance," and concluded "In my judgment Dr. Chun has been exploited by the Department." Overall, the Yip Report concluded that Chun had been exploited, though it found no evidence that he had been a victim of racism.
In 1998, Chun launched a $1-million lawsuit against the University for unjust dismissal.
A column by Margaret Wente of the Globe and Mail which attacked the settlement received severe criticism from many students and faculty.
The Arts & Science Students' Union (ASSU), which represents more than 22, 000 full-time undergraduate students at the University of Toronto described the incident as the "Dr. Chun miscarriage of justice" when bringing up the controversies of Prichard's administration, on the back of their 2001 Arts and Sciences Anti-Calendar.
In 2003, the Canadian Association of University Teachers (CAUT) established a committee to study Dr. Chun's case. They concluded there were “serious irregularities” in the hiring process in each case and that Dr. Chun was treated unfairly. They discovered when he had made allegations of systemic discrimination, he was subject to various forms of harassment and unfair treatment, such as being prevented from attending departmental meetings, denied a faculty library card, frustrated from pursuing his research, and prohibited from teaching courses. The inquiry described this as a serious violation of academic freedom.