(Old) Governments/Organizations

[Atsumari]

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Here is a list of groups mentioned more recently in the TNU Core Stories. More is on the wiki and countless other places.

Galactic Federation
The Galactic Federation or GFed or the Federation is a unified government of races created after Hukari Carain and Delta Force took down the United Universal Alliance of Republics and the Terran Dominion. The government is highly corrupt and has a system of government that is similar to a Federal Democratic Republic. Most of the organizations mentioned in the Core stories follow this government. Below is a list of the organizations which are under the Federation. The Federation use to be split up into the United Forces Alliance, United Universal Alliance of republics and various alliances. All were merged to create the Federation during the above mentioned conflict. 
Planetary Security Forces - Planetary Guard; think of them like the National Guard. Every planet has them; most of the time they are also the police forces. Not really seen much in the story just like they are not seen much in actual star trek.
Marine Corps -  there is a need for more than just security personnel. Marines handle ground based tactical operations and related missions. Usually work with Delta Force. 
Starfleet - Federation exploration fleet.
Delta Force Counter Terrorist Organization - the defense and special forces arm of the Federation it was branched out of Starfleet so Starfleet could focus on exploration though most people consider it still the same since it still follows Starfleet protocols for the most part (obviously since its a tactical organization it has exceptions as you have seen)
Armor Mechanized Corps (AMC) -  highly trained starfighter pilots; marines with starfighter certifications that fly mecha instead of starfighters.
Special Armored Division - Part of the Citizen Welfare Ministry. They handle outer rim security. 
Alchemy Commission - A special government commission under the direction of Delta Force, Starfleet and a number of civilian government agencies. They handle extremely advanced technologies that one would almost consider magic. They also handle all gems and similar technologies.  They maintain the Special Policing Unit a team of Special Investigators who handle "magic" or extra-physical type cases. 
Paranormal Response Unit - Renamed after the Chaos incidents. Handles Paranormal aces. Not really relivent to the story anymore.
Temporal Security Service (Temporal Directorate I believe they were called in Star Trek) - The time police.

Government Contractors
ITC A civilian contractor who builds things for delta force
Lonhorn A civilian contractor who builds things for delta force
Arvonus - Weapons contractor
There is a large list of these guys on ship design plans, mech design plans... Half of them are NEVER mentioned in story... 

Outside Organizations/Governments
AA (Aloris Alliance) - Far out government. It is not explained who is part of this alliance. They were mentioned in a mission when Misuki was sent to negotiate a treaty with them. They are led by one of the EU (Q) ascended Naomi Westbridge (Use to be a main cast member back in like 2006)
EU (Endormondon Union (Spelling I always fuck it up) - A faction of Q who control "universal" order.
United Watchers - An organization who just records happenings of time and space. Considered omnipresent.
WIS (Watchers intelligence Service) - The security and intel forces of the United Watchers.
Caldarian Union - They are a race that is near Earth II that is in rocky footing with the Federation. Better relations since the Federation became the Federation again.
Varaxian Union - Same as above; I could explain more but at this point in the story that information would be meaningless.
Klingon-Cardassian-Dominion-Rommulian Alliance - Basically before the federation came back into existence the Terran empire fucked over most of "nearby" space. Pissing off all the enemies of them enough to join forces. Once what is now the Federation (a bunch of other Terrans and other allied races) came back and recovered earth they tried to restore relations... Obviously that is ongoing.