Star Trek: 10 Things You Didn't Know About Section 31
6. Section 31 Wasn't Always Considered A Rogue Agency
During the 22nd and 23rd centuries, Section 31 worked closely with Starfleet. It was seen as a slightly shady but accepted department of Starfleet Intelligence. For example, they assisted the Enterprise with intelligence on the human terrorist organization Terra Prime when Terra Prime threatened to disrupt the founding of the Coalition of Planets, the precursor to the United Federation of Planets.
In the 23rd century, Section 31 was still overseen by Starfleet. Section 31 operatives traveled on Starfleet vessels and openly wore black versions of the Starfleet insignia that functioned as combadges. Starfleet admirals regularly uploaded reports to Control, Section 31's threat assessment computer.
By the 24th century, Starfleet officers saw Section 31 as merely a rumor or maybe an urban legend. Starfleet officers who actually encountered Section 31, such as Julian Bashir, reacted with revulsion. Their idealistic minds couldn't conceive of the existence of an organization comparable to the Romulan Tal Shiar or Cardassian Obsidian Order being part of the utopian Federation. Yet, as Constable Odo noted, while the Federation officially abhorred Section 31's tactics, they looked the other way when they needed the agency to do their dirty work.