It's happened before that the FBI had the goods on people, arrested them, showed their evidence to Justice Dept. prosecutors who agreed they had an airtight case and should indict these people--and then saw the whole thing fixed by higher officials. Read about the Amerasia affair of 1945. A foreign service officer named Robert Service had been living in Chungking with two housemates, one another U.S. official and the other a Chinese, who were both Soviet agents. When Service returned to the U.S. for several months in late 1944, he contacted two more senior officials in the State and Treasury Depts., both later proven to be Soviet moles.
Go-betweens also arranged for Service to meet a man named Philip Jaffe. Jaffe was an ardent Marxist with plenty of money who had a longtime interest in China. In the late 1930's, he had gone there with several other U.S. comrades and met with Mao Tse-Tung. Jaffe was the publisher of an obscure journal of Far East affairs called Amerasia. The OSS had discovered in early 1945 that the contents of one of its secret documents had appeared in this journal almost verbatim. When it searched Jaffe's offices, it found evidence implicating several other people, some private and some connected with the State Dept. State then called in the FBI, which started closely watching and listening in on Jaffe. And so when Service met Jaffe in a D.C. hotel room, their conversation was recorded. The two met several more times, and Service went to New York, where he hobnobbed with the people the OSS suspected were subversives.
FBI agents observed a five-hour meeting at Jaffe's house, attended by the head of the Communist Party USA and a known Chinese Communist agent. And they observed and heard Jaffe refer to meeting a known Soviet spy at the Soviet Embassy. The FBI then searched Jaffe's New York offices, where it found about fifty secret military documents it had overheard Service offering to provide. It then arrested Jaffe, Service, and four others its observations had implicated. But the fix was in. Conversations involving senior State Department officials and Truman's Attorney General himself were recorded, in which they arranged to fix things to get Service off.
A grand jury was convened, but the prosecutors rigged the game by presenting only the most innocuous parts of the evidence and downplaying them. They portrayed Service and the others as having, at the worst, used poor judgment in an attempt to help a journalist. And all six of the people arrested were no-billed. Years later, when this scandal began to come out, administration officials then lied through their teeth to cover up the earlier cover-up.