In a lit thread about voting in the Federation, I posted the following as a joke: Let's say you were a conspiracy nut living in the federation - what adventures of our heroes would you think were really secret conspiracies and cover-ups?* * I know we have seen actual cover-ups and conspiracies but let's stick to adventures that weren't but could be presented that way.
The Ferengi are only pretending to be annoying but otherwise harmless merchants to get into position throughout the galaxy. Once ubiquitous they will use their immense buying power to incite and direct intragalactic war and force the remnants thereof into perpetual indentured-servitude.
The Borg incursions were really just a ruse to tighten control of the population and to militarise Starfleet. Think about it, the Borg only attacked with a single cube at a time, did some damage but were then miraculously halted by the courage and tenacity of the "military" just before the Borg won. But these "attacks" scared the population enough that Starfleet was allowed to build Defiants, Promethus, Soverign class "star(war)ships" THe first contact incident was mearly propaganda with starfleet rigging a holoship to simulate a Borg Cube then a Borg sphere, the time travel part was faked to show that even history was safe in Starfleets hands. Think about it, we have seen the Borg throw dozens of ships to assimilate single Worlds or thousands to fight a war yet they send one at a time to assimilate Earth and why, Earth is not that important in the great scheme of things. Even the Federation is not. Open your eyes people, the Federation military-industrial complex is the monster not these "cyborgs"
Other way around, man. It's the matter from ass cancer that gets reconstituted as replicated food! Don't you see, man?! Replicated food is ass cancer! It's ass cancer!!!
In the ENT episode 'Bound' Captain Archer learnt that the apparent slave girls of Orion are actually running the operation. They feign getting sold to wealthy business men, then use their pheromones to mind control their 'owners' and take over their business. Now this discovery would surely have meant the end of this ruse once exposed. After all, what entrepreneur would willingly buy a slave knowing that within weeks she'd have stolen his business and placed it under the control of the Orion criminal groups? Yet we know Orion slaving is alive and well in Pike's time at least. Maybe longer. Clearly Archer and the Enterprise crew were convinced somehow to keep quiet about it. Indeed, as Pike himself considers going into business as a slave trader, it seems Star Fleet itself knows about the ruse, and keeps silent in order to get the occasional piece of the action.
Ben Sisko is no "emissary". Section 31 used certain subspace channels to send signals to him which caused visions of the so called "Prophets". This secured a partnership between Bajor and the Federation which advanced the goals of the Starfleet military industrial complex concerning expansion into the Gamma quadrant.
Q is king of the borg. That's right, he's Elvis. Elvis was abducted by aliens. The Talosians control Starfleet and Spock is a Romulan.
Looking at all the things that didn't make it into Starfleet records, orions, borg, ferengi, Archer's people were keeping quiet about a lot of things. With all the pay offs he received through the years, it's no wonder Jonathan Archer was one day able to buy the election and become Federation President.
You think section 31 actually exists, its just a boogeyman the Starfleet military industrial complex thought up to trick the populace into believing that all their schemes were the work of a rouge group that they are thwarting so as to make themselves look like heroes.
The Praxis explosion was caused by Starfleet Intelligence or the Tal'Shiar to waeken the Klingon Empire. Think about it - how can a mining accident cause such an explosion?