The scandal that brought down CIA director David Petraeus is now ensnaring General John Allen, the top U.S. commander in Afghanistan. The Pentagon says the FBI has uncovered thousands of “potentially inappropriate” emails between Allen and Jill Kelley, the woman who complained of harassment from Petraeus’ lover, Paula Broadwell. Kelley’s complaint to the FBI led to the discovery of Broadwell and Petraeus’ relationship, prompting Petraeus’ resignation on Friday. Allen succeeded Petraeus in Afghanistan last year. The Pentagon says Allen will remain the U.S. commander in Afghanistan for now, but that plans to nominate him to become NATO’s Supreme Allied Commander are on hold pending the outcome of an investigation. On Monday night, FBI agents continued their probe by searching Broadwell’s North Carolina home.