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Section 31 - The Outcome of Genesis.
Well, it was out.
Years and years of hard work holding the information in, making sure no-one got too involved besides those involved, and making sure that those idiots at Starfleet Headquarters saw the advantages of a new way to explore space because they were creating new worlds out of dead forms, like airless moons which had been floating through space for aeons, or planets with hostile environments could be converted and terraformed into a more suitable place for humans or other forms of humanoid life could live in peace, all wasted - Section 31's reasons for Genesis were a little bit more simple than what Starfleet could have come up with, but he wasn't concerned about that. All that he had to deal with now was just focus on the misery that Genesis had left in its wake.
Ironic since it meant creation.
It created something alright, a major mess.
Admittedly it wasn't Starfleet's complete fault, which was usually the norm since Starfleet's need to blunder into situations blindly caused more problems for Section 31, though it had the benefit of allowing their organisation to flex their muscles, even more, to seek out the enemies of the Federation and take precautions in case they had designs on the Federation - the Enterprise had managed to stop whatever the genetically engineered lunatic Khan Noonien Singh had planned, though granted Khans' need to get revenge on James Kirk had made the augment short sighted and inflexible, but not even those in Section 31 knew for sure what Khan had had in mind for Genesis after he and his band of fanatical megalomaniacs had managed to take over the USS Reliant. It was possible and likely Khan had planned to use the device to wipe out great swaths of life in the galaxy, but no-one could tell what was in an Augment's mind.
Starfleet had made a big mistake when they had quarantined the Ceti Alpha star system after the Enterprise first encountered Khan. They had done that for a variety of safety reasons, though Section 31 had foreseen ways Khan and the other augments could have escaped the system, and they would go on to carve an empire out of the stars. But it was collateral damage that something had caused the sixth planet in the system to blow up, reducing the planet to a perpetual wasteland.
But because of their shortsightedness, they had not bothered to inform Captain Terrell of the dangers. Oh, his first officer Pavel Chekov who had been on the Enterprise at the time of the attempted takeover of the ship when they had first stumbled across the surviving Khan and his brethren would have told Terrell of the presence of a secret human colony in the region, and who was in the colony. Unfortunately, because the Reliant hadn't realised like anybody else because Starfleet had virtually closed the place off about the places past, the crew had been overcome by Khan and his followers, all except the engine room company, who had been enslaved by a strange eel lifeform that made their victims susceptible to suggestion.
Khan and his followers had caused a lot of damage; the Enterprise crew didn't realise it at the time when the Reliant was destroyed after a textbook example of just how good a trained Starfleet commander was in the captain's chair, but when the Genesis device had been detonated in the Mutara nebula, it had caught the attention of the Klingons, and Commander Kruge had been dispatched to investigate. The Klingons really did keep watch on their enemies.
The Klingon Intelligence service had dozens of faults. Klingons were not like Romulans, they lacked the mental faculties needed to spy and keep information to themselves in large numbers whereas small groups could keep secrets easily and they had done successfully, otherwise their shithole of an empire would have died out long ago. Oh, they were okay with intelligence gathering during a war, but their fleets leaked intelligence like a sieve.
But locked away in their chaotic cesspit of an empire, the Klingons were really good at taking a good long look at their rivals, sitting in a web and gathering information about governments, scientific and engineering projects. Some of the projects were top secret with the people involved forced to live on site, but information could get out - a data transmission containing reports and logistics for someone at Starfleet to look over, which meant someone at Starfleet HQ could get curious and try to dig even deeper - actions like that usually attracted unwanted attention and raised red flags for organisations like Section 31 or the Tal Shiar, or it could be something as mundane as someone like an admiral going out on an inspection tour, or a letter being intercepted to someone's family.
But Genesis had blown up.
Something like that had raised dozens of red flags. The only people in the Federation to know about the illicit and top-secret project had been the Federation Council, the science council, those involved obviously who were among the top minds, and high ranking Starfleet officers who had the clearance, and afterwards the cadet crew of the Enterprise.
But Starfleet had overlooked the fact an entire nebula had been blown up, and the energy had been funnelled to create and terraform a brief earth-like planet. Did they really think the Klingons would not overlook something like that? No, they would get it into their heads (sometimes many in 31 cursed the Hur'Q, whoever they were, for making Klingons xenophobic and suspicious to the point where they lashed out all the time) that the Federation was experimenting with weapons. The Romulans had as well, but unlike the Klingon High Council who had demanded instantaneous information from Kruge, the Romulan Senate had ordered the Tal Shiar to investigate as well, but the minds behind that organisation had used their common sense to do so quietly.
Nothing the Klingons did was quiet; they bulldozed their way into Federation space, using a cloaked ship. They had their informants go through their contacts, looking into the information, and Kruge killed someone important to him to cover his tracks. To make it even worse for the diplomats, Kruge and his ship destroyed a Federation starship. The Grissom had been no match for a fully armed Bird of Prey, but it had sent up red flags when Starfleet command, furious by Kirk's theft of the Enterprise, had sent messages to the Grissom but received no response.
Captain Esteban had been a by the book officer, not a maverick like Kirk. He always responded to the messages and sent reports every minute to keep HQ appraised during a mission.
The silence had been noticed but it wouldn't be until later, when the Genesis Planet had been destroyed, reduced to pieces that would be drifting through space to create new planets, so ironically while the project was essentially a failure now Dr David Marcus had been using protomatter to cut corners, the project would succeed only it wouldn't be in the lifetimes of anyone in the 23rd century, that the Grissom had been destroyed by Kruge when Starfleet detected the Bird of Prey, stolen by Kirk and heading to Vulcan.
But in the three months since the incident before the Whale probe entered Federation space and left behind a number of powerless and helpless starships drifting through space, Starfleet, the Federation Council, and Section 31 had been working hard to mitigate the worst of the disaster.
You had to hand it to Kirk, he truly got the ball rolling.
He may have been troublesome, but he was good.
Dr Carol Marcus had been forced to answer for what had happened, and the questions had been going in thick and fast when it was revealed by Starfleet who had finally sent ships to investigate the sudden disappearance of the Grissom and her crew, and the destruction of the Genesis planet, had detected surprising amounts of protomatter.
Section 31 had known about the secret protomatter acquisitions, but they had left them alone since any interference might risk discovery that another organisation was taking notice, but 31 had been on the alert and had always been prepared to silence anyone who caused trouble.
The diplomats were also busy dealing with the outcome.
The Klingons, in their typical brazen manner, had revealed the existence of Genesis and how dangerous it was. They also called it the Ultimate Weapon. Typical Klingon arrogance, but they had a point. There were quite a few militant members of Starfleet who had seen ways Genesis could have been used to devastate or destroy any enemy that came around the Federation's way. It would have been for the Greater Good, though the lines could blur if planets were destroyed, the life irretrievably destroyed by the Genesis Matrix.
The Klingons had also proudly admitted to the destruction of the USS Grissom, dressing the whole thing up as an attempt by James T. Kirk as a way to destroy the Klingon Empire. It never failed to amaze Section 31 just how egotistical the Klingons could be, but there was nothing they could do, but they found the Klingon Ambassador's claim there would be no peace as long as Kirk lived as both tempting since Kirk caused plenty of trouble and yet helped Section 31 in more ways than one, but also a bit too far, even by Klingon standards.
Section 31 wasn't even going to try to suppress the existence of Genesis. It had been decided. It could be quietly buried until no-one knew about its existence, but someone could find out about it by word of mouth and passing it down through the generations.
The Genesis Project had several applications that Section 31 could have used in furthering their own agenda, but maybe it was a good thing that it had failed.
Only time would tell.
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A/N - The way I see it, many in Starfleet saw Genesis as a weapon despite the organisation's peaceful leanings, and Section 31 was always happy to take steps to protect the UFP.