The secret bonus scene was originally shot for the Star Trek: Discovery Season One finale episode "Will You Take My Hand?" but was cut from the episode and held aside for a special occasion like WonderCon.
The scene takes place sometime after the aborted mission to destroy Qo'nos. Former Terran Emperor Phillipa Georgiou is now running a bar in the Orion compound on Qo'noS. She is approached by Leland. He is disguised as a Trill, but Georgiou easily sees straight through his act. Leland is actually a human, and Georgiou assumes he is a Starfleet agent sent by the Federation. Leland offers Georgiou a chance to use her skills to the fullest and shape the new universe she finds herself in. He gives her a black Starfleet badge and welcomes her to Section 31.
The black badges first appeared in the third episode of Star Trek: Discovery, "Context Is for Kings." Fans speculated about what the badges could mean since they had never been seen in Star Trek before. Combined with Discovery's serial number, NCC-1031, some fans felt like the evidence pointed towards Section 31.
The theory lost some steam after it was revealed that Discovery's sister ship, the USS Glenn, had the registry number NCC-1030. The numbers were strange since the Enterprise's registry is NCC-1701, but the Glenn and Discovery numbers seemed sequential rather than purposely meant to hint at any other connections.
Captain Gabriel Lorca was also speculated to be part of Section 31 since his leadership style so unorthodox for a Starfleet captain, but he ended being an agent of the Terran Empire from the mirror universe instead, seemingly putting the Section 31 theory to bed.
But the black Starfleet badges were never explained. Some figured it had something to do with Discovery's top secret "black alert" protocol for operating the experimental spore drive, but it turns out fans were right the first time and that the black badges are the insignia of Section 31.
Section 31 is a secretive organization that operates with Federation interests in mind, but without any oversight from the Federation or Starfleet. The organization takes its name from the section of the Starfleet charter that allows for extraordinary measures during times of extreme threats. The organization was introduced in Star Trek: Deep Space Nine and then further explored in Star Trek: Enterprise. The Kelvin timeline version of the group was a major factor in the movie Star Trek Into Darkness.
Star Trek: Discovery begins filming its second season in Toronto in April.