Formed in the ashes of the Eugenics War from all of Earth's intelligence agencies such as the FBI, CIA, MI5 and MI6, Section 31 is an officially nonexistent and rogue organization, branching loosely from Starfleet Intelligence. The group wasn't acknowledged by either Starfleet Command or the Federation government. According to one operative, the organization dealt with threats that the Federation knew nothing or very little about.

By 2598, Section 31 had been eradicated. As they kept no permanent documentation, members of the group were hunted down by the Federation, where they forcibly had their memories extracted. This caused a public uproar by various member species of the Federation, who deemed the act is "inhumane". Medji Crassana, president at the time, defended his actions, stating that it was necessary "to protect the future of the Federation".

The memories that were taken were stored in a memory buffer on the planetoid Anaura, which was located deep within Tholian space. In 2598, the Federation starship USS Pioneer, captained by Edward Mantree, was ordered by Federation President Lorel to retrieve the information.

Before the Pioneer went to Anaura, only the president, the Commander-in-Chief of Starfleet, and the Head of Starfleet Intelligence were allowed to know the location of the memory buffer.

Section 31 was also known by its members simply as "31". (PIO: "On a Knife Edge")

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