Eventually, the Enterprise is assigned a rescue mission. A science guy on an outpost near the Romulans got himself into some shit with the locals and the Federation would like to avoid a violent misunderstanding. The Enterprise sets out, and when they get there do a pretty typical heroic thing - they battle some angry aliens, find the scientist, and recover his stuff for him. Aboard the ship though, they find that some of what the scientist had is odd. There are tools, weaponry of a kind they haven't seen before, that do things uncharacteristic of Federation technology. The scientist denies knowing much about it, but it's clear from how they're engaging something is being kept from the Enterprise crew. The guy knows more than he's saying, but because he won't explain all they can do is take him back home and hand over what they found.

When they arrive at a starbase and check in with Starfleet, the captain is puzzled by their reaction to his report. They acknowledge what he found, but offer no real explanation/details. He's told it's simply not part of his mission to know. Before they're done, he checks out the equipment one more time, and discovers an insignia - Federation Security, the apparatus that grew and expanded during the Dominion War. Federation Security didn't disappear when the war ended, but its role was greatly reduced. A landmark moment in that history involved a new civilian government legislating various constraints on its activities and paring back the surveillance machinery built up for the Dominion War. The captain is puzzled why this organization would be operating on a remote outpost at the edge of the territory, and tries to investigate further. He finds bits and pieces, communications to and from the outpost in an indecipherable format. He tries to find out more about the scientist, and discovers he has always been in close contact with various structured linked to Federation Security. Those monster-of-the-week encounters were all also associated with the scientist's work - he was communicating with them, and to some degree may have orchestrated some of the moments the enterprise was sent there to resolve.

Before the captain can put things together though, they receive orders to head out again on another mission near Romulan space. Along the way, strange things begin to happen. System failures, computer glitches, mechanical problems crop up and no clear explanation for them emerges. When the Enterprise reaches its destination, they are unable to locate the folks they're meant to rendezvous with. They try to reach Starfleet, but their communications start screwing up, and the engines become nonfunctional. As the crew tries to work out what is going on, multiple explosions rock the ship. Cloaked vessels are firing upon it, and the system malfunctions mean the Enterprise is more or less adrift. The ship is badly damaged, but in the nick of time engines get restored and they warp away. They set off for a starbase, but without the ability to communicate out to anyone.

When the Enterprise makes it to the starbase, they come to find this incident is already known to everyone. Across Federation space it's been broadcast that the Enterprise was attacked by the Romulans. Though it's unclear exactly why they would do that, the incident is such a surprise that folks are scared, and leadership is saying this portends a larger conflict if the Romulans don't have a good explanation for what happened. While the Enterprise is docked, the captain/crew try to get in touch with Starfleet to inform them of what happened, but everyone they speak to seems dead set on seeing the incident as an unprovoked attack. The system malfunctions and original mission details aren't being included in folks' accounts of what happened and they won't correct their stories after hearing from the Enterprise crew.

On their own, the captain and crew try to figure out what they can about the vessels that attacked them. The Enterprise didn't pick up much, but what little it did seems to indicate weaponry in some way similar to the weird stuff they found when they rescued the scientist. Before they can land on anything definitive, repairs are completed and Starfleet orders them out to rendezvous with other ships to help prepare for a border operation. Before they leave the starbase, the captain alone in his office is approached by Federation Security. He is told, they know of the particulars he's been trying to communicate, but they are ordering him to stay silent about the reality of his encounter. He must also ensure his crew stays silent too. If he tries to defy these orders, they will be removed from their posts. The captain, knowing at this point how wide the narrative has been broadcast about the attack, reluctantly agrees. The Enterprise then sets out for its next mission.

While the Enterprise is en route to the other Federation ships, the captain can't help but be fixated on that encounter with Federation Security. Something has to be afoot, but given how quickly everything evolved since the encounter with the cloaked ships, he knows he has to work out what to do on his own. As the Enterprise travels between systems, picking up different missions and coordinating with other ships, he notes areas in space where their communications will be less effective, and takes those moments to conduct investigations. During some of their encounters with the other ships, they meet people descended from characters in TNG/DS9/VOY. Through these characters, the captain comes to learn about stuff that never got told to folks, like the 29th century time traveler, covert operations surrounding Deep Space 9, etc. He learns details about what happened with each of the other Enterprise vessels, and is made to confront the idea that his Enterprise isn't like those. Those really were about exploration and discovery; his is more of a pawn in a larger scheme, the resurrection of an old image to serve a malign end.

The captain becomes convinced, there is something deeply wrong with what is happening - Federation Security seems to have a much larger role in the Federation's leadership than what was known to most people, it didn't lose the power it had accrued. At this point, the captain pulls together his most trusted crew members (the bridge crew, basically) and lays out what he's come across. The Enterprise continues its missions, and when another opportunity to work in secret presents itself, they get together.

They determine the cloaked vessels were in fact using weapons identical to the kind they found with that federation scientist. The tools he had were for intercepting and altering communications. The Romulans don't appear to have been doing anything of note anywhere near the part of space where they were attacked. As they get the details straight, a dark truth begins to emerge - Federation Security, not the Romulans, attacked them, utilizing cloaking technologies derived from some of the weird 29th century shit Voyager came across. They were attacked so as to give pretext for a conflict with the Romulans, which would mean a newfound need for Federation Security to take up a leading position within the Federation power structure. Much of the history they understood simply wasn't true - while on the surface, the Federation backed away from security/surveillance, in truth these aspects were being consolidated behind the scenes using much of what prior Enterprise excursions came across.

The captain and crew decide, they have to reach the Federation's civilian leadership with what they've uncovered. They quickly come to see though, that will not be easy to do. Their investigation allowed them to understand some of how Federation Security operates, and in a revelatory moment they see that Federation Security is practically everywhere. They can observe what the crew does on their ship computer, they can see through the cameras, everything they're doing can in some way be observed. As its dawning on them that their entire effort has probably been seen, the Enterprise comes under attack.

This time, it's a fleet of Federation ships. Communications are established, and the captain is told they are being apprehended for having sent sensitive information out to the Romulans. The captain and crew know, this is a setup, and so instead of surrendering they fight back and haul ass toward the nearest edge of Federation space. They escape. The ship is damaged but still functional, and once past the border their pursuers eventually turn back. Alone, in need of repairs, the Enterprise charts a course to an unpopulated system.

With the Federation now hostile to them, and without means of getting in contact with anyone inside the Federation, the Enterprise crew devises a plan to get their ship fixed up and contact the other, non-human species within/around Federation space. The Klingons, the Romulans, the Vulcans, so on and so forth. They work on outfitting a shuttle to be able to cross borders undetected, so they can get to the various homeworlds and see if they can inform these species of Federation Security's scheming.

With each encounter, they outwit and fight it out with the intelligence apparatus of each species, in stories based on wild shit actual intelligence agencies did. For example, in one episode they pick up some supplies only to find they've been laced with poisons. They reach the Klingons and have to deal with the Klingon KGB thinking this is all some triple agent stuff. They reach the MI5 Romulans and have to throw off pursuit by cloaked ships. They make it to Vulcan in disguise and feed false information to their Federation associates. Lots of room for half-monster-of-the-week material. In the end, they manage to reach important people with each species, and come out with a new plan to get the truth broadcast to the whole of the Federation all at once.

A coalition of ships, outfitted for secrecy/evading detection, along with a similarly outfitted Enterprise, will penetrate into Federation space on a course toward Earth. Using every dirty trick, they will attempt to distract and throw off Federation Security enough for the Enterprise to make it to Earth's big communications relay, where they can broadcast to everyone the truth of Federation Security's false flag op. They're under the gun, because while they've been doing all this the Federation has been gearing up for a bigger conflict. The border with the Romulans is destabilizing, folks are getting in petty skirmishes, the populace is being brought to thinking they must go and fight. If they don't make it in time, the war will begin proper and there's no telling where that will go.

The coalition fleet assembles, pinpoints where they've got the best chance to cross back into Federation space, and get going.

Eventually they get near the Sol system. The Federation's warships are all over the place, with enough firepower that the Coalition Fleet stands no chance in a direct encounter. Through the use of all their weird intel agent tools they manage to evade detection and throw off pursuits, but not without some having to escape and others getting destroyed. Eventually the time comes, where the Enterprise alone has to get to Earth while the fleet performs a distraction.

The Enterprise nears the moon, and figures out a way by which they can evade detection by maintaining a stationary orbit in a spot of weird stuff in between moonbases (I gotta technobabble that one I'm sorry). The captain and bridge crew man a shuttle and head out for the communications array, a big structure in between the Earth and the moon (again not sure whether that exists but let's just say it does).

At the array they encounter almost no resistance. By now they know, something is up, but they have to complete their mission so they keep on. The goal is to send out a broadcast through the array that provides irrefutable proof of what they've found about Federation Security's attack as well as what information they could put together from their encounters up to this point. The hope is that once this is out there, Federation Security will lose enough credibility that it will be isolated - the rest of the Federation will hopefully turn against it.

As they near the station they need to use, they are stopped by Federation Security's topmost people. They're offered a deal - surrender, hand over their information, the captain will be put on trial and the crew will be spared. For a moment it's uncertain how this will play out, because the experience of getting to this point has been one of continuous paranoia, suspicion, betrayal and exhaustion. However, together, they refuse, and fight it out while the captain and first officer get to where they need to be to get the broadcast done.

They succeed. The Federation, all at once, is informed of what has happened. The remaining ships of the Coalition Fleet phone home, and ships from all over the quadrant approach to take down what forces Federation Security can muster. Most of the Federation turns against FS as well, so their leaders get apprehended and their power structure dismantled. The captain and crew, exhausted, head back to the shuttle, board the Enterprise and reveal themselves to the wider populace as this coalition effort secures the space.

The show picks up again a few years later. After this incident, the Federation underwent a radical stage of transformation, in which the warmongering security apparatus was taken apart for good. In doing so, there were times of difficulty and disagreement - the other species came to learn of stuff that made relations harder to maintain, but because of the Enterprise's efforts in 2540 these ultimately were resolved. The captain and crew were eventually lauded as heroes of Federation, though none took up positions of leadership. Instead, many of them resigned, to live as civilians after having seen a bit too much. The captain stayed for a time, but eventually decided it was best for someone else to captain a new model, one that could conduct its exploratory missions without the burden of having been at the center of a big nasty scheme.

THE END

If I could summon infinite money and good actors, I think I'd focus a lot on the idea that following the end of DS9, the Federation wasn't quite the same thing as before their war with the Dominion. My read of DS9 was of the Federation slowly transforming into a security state - it was losing some of its freedom and exploratory nature for the sake of defending itself. By the end of DS9 it felt like the Federation had lost some of its spirit, and was left in a situation where it needed to seriously interrogate what it was all about. Voyager went further along in time but I don't remember it having much to say about the state of the Federation broadly.

My beef with post 2005 Trek (as in, after Enterprise was over) was that instead of heading on into the future the franchise kept going back. I wanted to know, what happened to them after the war was done, when the need for surveillance and security fundamentally changed. Did they just go back to being about discovery and science and stuff, or did they go down a paranoid, Terran Empire sort of path? I think either could have been interesting, but more importantly I think leaving off with that kind of uncertainty was a good setup for doing a show that would have landed real hard years down the line. We all lived through the emergence of things like mass surveillance and the algorithmic internet and I feel like Star Trek should have been there to show us some of what could be done with that. I would like to hope that if a deep truth got sent out into the world it would mean something, so that's what's in what I wrote here. I think there would be a lot of room in a show like this to reexamine the role of the stuff we experienced, grew up with, etc., through the lens of an Enterprise captain realizing his mission isn't what it appears to be.