Floyd I. Clarke, the No. 2 official at the Federal Bureau of Investigation who operated for most 1993 as the agency's de facto director, said today that he would retire in January to join a New York company led by the financier Ronald O. Perelman Mr. Clarke said he would become vice president for corporate integrity at MacAndrews and Forbes Holdings Inc., the investment group led by Mr. Perelman, the one-time corporate raider. Mr. Clarke rose from a street agent to become the agency's chief day-to-day operating officer, overseeing the agency's worldwide criminal investigative operations, budget and administrative operations. He was deeply involved in planning the ill-fated tear gas assault on the Branch Davidian compound in April. Officials said his departure was not related to a Justice Department inquiry into a 1992 standoff between the F.B.I. agents and a white separatist in Idaho. Many senior officials regarded Mr. Clarke as the man who ran the agency in the turbulent months before President Clinton dismissed William S. Sessions as Director in July. Mr. Clarke served as interim director before Louis J. Freeh was was sworn in to head the bureau in September.