In the movie, Star Trek: Into Darkness, the audience sees Khan putting two large duffel bags in the truck of a vehicle. This was mostly unnoticed by the chaotic crowd of bystanders. But Kirk, viewing the footage of the carnage, asks the council members, “What’s in the bags?” Suddenly, Khan attacks the building, killing Admiral Pike. The question went unanswered in the movie.
What is Section 31?
To answer the first question, we, first, have to examine, “What exactly is Section 31?”
In days long past, in a parallel dimension, there was an Earth that was destined for greatness. It started out much like our own. They had hopes and fears like the ones we have now. Just like us, each country had their version of Homeland Security. The many countries on this Earth formed unions. Each of those Unions combined their Homeland Securities into larger facilities. Then, as those unions formed into Hemispheric factions, they joined their Securities into larger facilities. By the time, this Earth each the early 1980’s, it was one of these faction’s security facilities that created the Super Beings. This lead to the Eugenics wars.
It was after the Eugenics Wars that Zefram Cochran invented the first warp drive. On his first voyage, Zefram managed to be noticed by a Vulcan Ship. They came and introduced themselves. In time, the Earth became part of the Federation. With their help, Earth stabilized and gained the ability to govern itself. It was during these years that information was gathered from the Security Sections from the extinct government factions. This information was kept in a new, centralized system called Section 31. Section 31, was located under the Kelvin Memorial Archive, which is our equivalent of a public library. Section 31 is a highly secured governmental department that holds top secret and highly classified information on research and development and all the information regarding timelines, including alternate timelines! As we know from the movie, the archive was blown up by Noonien Khan.
Star Trek: Into Darkness
A short time later, during a meeting in the Daystrom conference room at Starfleet Headquarters, Kirk asked, “What’s in the bags?”
There is no response and the question is never answered by anybody in the movie. So wrapped up in the action scene that follows and the death of Admiral Pike, Kirk completely forgets that this even happened. Which is understandable for Kirk but Spock was in the meeting room too. Spock would not forget that Kirk’s question wasn’t answered. It is highly likely that Spock, went looking for the answers. Spock would not have been able to look for those answers in the movie, Into Darkness. But the moment he had time to investigate, Spock, like his ancestor, would have taken up the case.
What’s in the bags?
It’s a cryo-chamber, of course, one in each bag. Each cryo-chamber holds about 5,000 Eugenics embryos. Which gives us our 10,000 count from Enterprise, Cold Station 12, Borderland. Of course, Noonien Khan found them in Section 31 while working on the Juggernaut Warship! Marcus even tells us during the meeting. He mentions “the attack on Cold Station 12.” This is a second attack. Arik Soong had already attacked Cold Station 12 years before. It was this attack that leads the Klingons to a small number of Eugenic embryos. The Klingons are not specifically looking for more embryos, they are looking for something else. They are looking for information not located on Cold Station 12.
Khan stole Arik Soong‘s work. Captain Archer tells Arik Soong (Data’s grandfather) that his work is not being destroyed. The work is being held in Section 31 for further study. This happened years before the destruction of the USS Kelvin. Additionally, Admiral Marcus and Noonien Khan had access to information regarding Julian Bashir. We know this because the juggernaut warship actively shows armament and maneuvering capabilities equal to or greater than the Defiant. Julian Bashir is the only known stable Eugenics survivor in the history of the franchise. Julian Bashir also studied the eugenic issue, with little success. It only makes sense that while Khan was in Section 31, he downloaded it all, and took the work and the remaining embryos to the Klingon homeworld. The vaccine by Dr. Phlox did not cure the mutations or the plague, it only halted them in the first stages. The Klingons want a cure for the plague and they want it at any cost. This leaves a burning question for every Sherlock in the geek world, “What did the Klingons give Noonien Khan in return?”
For the Future
This information might have a huge effect on the upcoming movie. The Klingons didn’t just experiment on other Klingons with the embryos and Arik Soong’s work. They experimented on other species in the Empire. Because the Klingon Empire is, currently, in an unstable state, the Klingons cannot contain or patrol their Empire as they normally would. It is safe to suspect that the borders of the Federation and the Klingon Empire is, at the moment, very chaotic. If the Klingons experimented on worlds close to the border, we might expect one of those worlds to rebel and go rogue. Would that world attack the Federation?
And what of Spock? His investigation into the bags may have led him to a planet, within the Klingon Empire. If he is captured, it may be up to Kirk and the crew to search for him, and possibly rescue him. This is a dangerous prospect. The Federation doesn’t have good relations with the Klingon Empire at the moment. If the crew gets caught by the Klingons, it would be very bad. If the inhabitants of another world within the Empire have him, Kirk may have to violate the Prime Directive to retrieve him. We can only wait and see what happens next.