Third, at the point the FBI learned of the Petraeus affair, they were still in the middle of an ongoing criminal investigation. Had they shared the information they discovered with officials in the administration or on Capitol Hill, they risked allowing political interference — or the appearance of political interference — to taint what was an active investigation into whether laws had been broken. Ironically, had the Justice Department briefed the White House at this stage of the investigation, there would be aggressive questions from Capitol Hill today into whether the White House had somehow squashed an investigation into the CIA Director’s girlfriend before it was completed or delayed its conclusions until after the election.
Instead, the FBI proceeded with its investigation until it satisfied itself there had been no breach of national security. At that point, they faced the unusual situation of what to do with the information about General Petraeus’s extramarital affair. In nearly any other case, they would simply close the investigation and move along. The Department of Justice makes legal judgments about whether laws have been violated — not moral judgments about the propriety of extramarital sex, and not policy judgments about the fitness of government officials for service.
Ultimately, once Petraeus had admitted the affair, they determined it was appropriate to inform his direct superior, Director of National Intelligence James Clapper so he could decide, in consultation with the White House, whether Petraeus could continue in his position.