From the original Third College demands, UCSD administration initially allowed direct student democracy and oversight, in line with the focus on self-determination.

The original 1969 demands explicitly outlined that Third College be governed by a student-faculty board, specifically that the "Board of Directors" consist of "two students, one faculty members, and the provost." Further, students who served were to serve for a twelve month term, be recalled by majority vote of the college, compensated at a rate of 125% of the average yearly income requirement of a college student at UCSD, and given credit for one normal course per quarter applied towards graduation.

In 1970, when Third College was established under inaugural Provost Joseph Watson, the demands for the college to be governed by significant student input appeared in the Third College Academic Plan only briefly. The proposal did not explicitly mention the Board of Directors, and thus the Senate did not formally authorize a student-led Board of Directors. This decision was strategic, made in order to increase the chances of the Academic Plan gaining the UC Regents' approval of the many then-radical ideas surrounding the establishment of Third College.

In the first two years of its establishment, Third College was as the demands of self-determination intended: "...with exception of faculty recruitment and program development, students had a voice and vote on every level of the College's governance, beginning with the General Assembly, Committees of Admissions, Curriculum, Community Relations, Construction and Design, and the Board of Directors" (Moreno, 2009, p.306). Although most students did sit directly on a committee or leadership role, many participated in the General Assembly, made up of undergraduates, graduate students/teaching assistants, staff, and faculty meeting monthly in an open forum.

Unofficially, the Board of Directors existed as the "unofficial executive body" governing Third College through the Third College Academic Plan's approval and the adoption of College By-Laws in Spring of 1971 (Moreno, 2009, p. 308). The UCSD Chancellors, UC Regents, and Governor Ronald Reagan were disapproving of the Board of Directors and warned Provost Watson that he would be responsible for the College. 

In practice, the Board of Directors were the main governing body, and the student slots were reserved for one African American, one Chicano, and one "other", which meant white, Asian American, and Native American students lacked a definitive representative. Thus, during the drafting, many of the three groups fought for expanded Board membership, while many African American students present opposed the proposed measure since Black and Latine students had founded the College's student body. Watson also opposed expansion, wanting a smaller group for easier discussion and negotiation.

Tensions later rose throughout 1971 and 1972, with Watson asserting his power over the Board of Directors and General Assembly. He fired a popular Chicano Admissions Officer against the Board of Directors' wishes, and on other occasions, Watson was the lone no-vote on prospective faculty selection. Since the Board was ruled on unanimous decision, this effectively rendered them unable to recruit desired faculty.

Eventually, Watson told the Board that if they disagreed with him, they should take it up with the General Assembly; a majority Assembly ruling proposed amending the Board from unanimous to majority vote, which Watson opposed. In Spring 1972, a coalition of student leftists across races voted for his resignation as Provost of Third College, citing his opposition to the demands for self-determination and equal representation. Notably, the Black Student Union (previously the B.S.C.) pledged loyalty and support for Watson.

Soonafter, a Lumumba-Zapata Steering Committee was formed out of Movimiento Estudiantil Chicanx por Activismo (MEChA), Asian American Student Alliance (ASSA), United Native Americans (UA), and the Third College White Caucus. The formation led to hunger strikes, rallies, community meetings, and pickets, and eventually Watson resigned before withdrawing his resignation and continuing on as Provost at the urging of Chancellor McElroy. Tensions heightened as student leftists, the organizers of the original protestors, were more united than the cultural nationalists; racial frictions as well as competitions for government resources worsened.

Strained relations and close calls with racial violence followed. Students believed that law enforcement took advantage of that division by placing agent provocateurs to heighten racial tensions and an illegal break-in to the University Contracts Office by a white radical student group revealed an agreement by the UCSD Administration and the Federal Bureau of Investigation (FBI) to allow fifty undercover agents on campus (Moreno, 2009, p. 317). Paranoia of bugging and informants among their ranks rose among the leadership of the organizations, although the majority of Third College students still developed interracial camaraderie.

On May 18, 1972, the UC Regents responded to the calls for Watson's resignation by passing a resolution declaring all student government bodies across all UC campuses were official units of the university and operated solely under administration authority. Student activity fees and assets belong to the university, and university administrators retained ultimate veto authority.

When Dr. Watson withdrew his resignation in June of 1972, he did so under the condition that he would retain full authority over the college. Thus, with the Board of Directors never being formally recognized, it was dismantled and replaced by an advisory committee, which eventually evolved into Thurgood Marshall College Student Council. This was met with faculty and student withdrawals and protest, especially among Chicano faculty and MEChA. By the late 1970's, Third College was no longer minority oriented, unable to sustain a one-third Black, one-third Chicano, and one-third other balance. 

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