So that I don't have to explain Checkmate/etc stuff to everyone individually, here's a big infodump about WTF everything is. If you have questions and whosits and whatnot, ask away and I will try to clear things up. :uhoh
(this stuff will go on the wiki eventually, but for now it's here!)
...the Justice Society?
During the "Golden Age of Heroism" (which for our purposes is the period from WW2 through to the end of the Space Race), a group of adventurers, private investigators, detectives, government agents, and a weirdly large number of archaeologists became costumed superheroes in order to fight against the Nazis, the Commies, and their supervillain associates. This is like the beginning scene of The Incredibles, or the Bob Dylan flashback sequences from Watchmen: everyone's costumes were a little bit goofy looking, everyone had cheesy names and gimmicks, and the American people (and government) were pretty much on board with superheroes doing their thing in campy '60s Batman sort of ways.
A lot of these old 40s/50s characters have been reintegrated into the modern DC timeline as living on "Earth-2" where the time streams don't sync up, which is why we're seeing the 1940s Jay Garrick interacting with Barry Allen as if they are more or less contemporary on The Flash.
Several of those heroes banded together as the Justice Society of America. The government was relatively okay with this (after all, the more vigilantes you can convince to join the JSA, the easier it is to keep tabs on everyone), and sort of "endorsed" the Justice Society. There are probably a lot of old photos kicking around of mayors and senators and Attorney Generals shaking hands with members of the Justice Society for the sake of political capital.
Unfortunately, it all fell apart during the 70s (ish). Like in Watchmen, the government probably wanted it's heroes to go fight in Vietnam the way they had during WW2. There was the Watergate scandal. There was economic problems, trouble in the Middle East... everything started getting bleaker. Some heroes (like Alan Scott, the original Green Lantern) decided that they were too old for this shit and went into retirement, and there weren't any young people around to replace them. A few terrible things happened, like the death of Hawkman's wife and of Doctor Fate's original host body, and the subsequent "theft" of Hawkman's son as Fate's new body. Some of the heroes might have been forcibly retired by the government for various reasons, a la The Incredibles.
And then there's the final batch of Golden Age heroes, who went on to found Checkmate.
...Checkmate?
Several figures from the heroing community - Jay Garrick (the Flash), Rex Tyler (Hour-Man), and William Glenmorgan being three of them - realised that they couldn't keep the world safe wearing tights and capes any more. A lot of the Golden Age heroes were either industrialists and/or government agents, so they merged the two, using their businesses to finance a semi-official spy agency that would continue to protect America from Communists, and then terrorists, and then metahumans. If they took down a science villain with cool gadgets, they'd reverse engineer them and profit from the technological advances, feeding that money back into funding their operations. They're basically the Men in Black I suppose, except instead of "worst scum of the universe" they're protecting against spies and terrorists - so sprinkle some 24 and Homeland inspiration in there... or Section 31, if you're familiar with Star Trek.
As the war on terror escalated, Checkmate has escalated it's methods to match. When Oliver Queen "died" ten years ago, Checkmate acquired his company, and has been playing a high stakes game of corporate Pac Man, gobbling up all of the businesses that Checkmate already controlled, and engaging in hostile takeover of vigilante and villain businesses that have patents that Checkmate needs. Somewhere along the line though, Checkmate crossed the line into "ends justify the means" territory. They will often intercept minor villains, and offer them the opportunity to come work for Queen Consolidated's secret R&D division instead of going to jail. The Suicide Squad (which takes dangerous supervillains and sends them on suicide missions in exchange for reducing their prison sentence) is also a Checkmate thing... sort of.
In addition to controlling Queen Consolidated directly, Checkmate also has influence over various other groups: think HYDRA, and the way they positioned people in different aspects of government. The Director of ARGUS is an ally of Checkmate, as is the Attorney General (who is the boss of the DEO Director). There are probably Checkmate operatives and allies within STAR Labs, the GCPD, Wayne Enterprises, Gotham City Hall, and just about everywhere else. Checkmate are puppeteers, and they have strings attached to everything.
It's important to remember though: Checkmate does not see itself as evil. They are CIA black sites, Guantanamo Bay, and "desperate times call for desperate measures" taken to the ultimate extreme, but they do want what is best for America, rather than having any murderous world domination schemes.
...ARGUS?
In our world, ARGUS - "Advanced Research Group, United Support" - is basically the agency that does all the Area 51 stuff. They were set up by the Department of Energy in the wake of all of the "lets experiment with nuclear energy... oh shit we created a supervillain" antics of the Seventies. If there is something dangerous out there in the world - technology, magical artefacts, powerful metahumans - their job is to find it and lock it up. In that regard they're very similar to SHIELD, or to Team Flash. ARGUS uses two main facilities to lock stuff up: they control the exclusion zone around Area 51, and have a big Indiana Jones style warehouse where they shove all the dangerous "things"; and in Belle Reve in Louisiana they have a "Supermax" prison to hold all the metahumans and supervillains who are too dangerous to be held at regular facilities.
In addition to having a bunch of retrieval teams (Team 7, the Secret Six, etc) to gather up all the dangerous stuff, ARGUS also facilitates some amount of research, though under a HUGE amount of scrutiny and supervision. Area 51 is the military's research facility within the Nevada exclusion zone, while Mercury Labs in Mercury, Nevada is the STAR Labs facility on site.
Though ARGUS is not part of Checkmate, they are secretly allies: the Director and several key personnel are part of Checkmate's spy network. Among other things, ARGUS will issue a government contract to Queen Consolidated to help them research anything "cool", so that QC can sneak data back to it's own covert research programs. Also, Checkmate "borrows" prisoners from Belle Reve to be part of it's Suicide Squad, so ARGUS (sort of) shares responsibility and authority over the team.
The identity of the Director of ARGUS is classified, and they are known only by the codename "Mockingbird" (think M from James Bond). The Director is probably Amanda Waller, but don't mention their name just in case it ends up not being.
...the DEO?
The Department of Extranormal Operations are an agency set up to police metahumans, aliens, magic people, and vigilantes within the United States - in an FBI / Homeland Security sort of way. They have a "needs of the many outweigh the needs of the few" sort of attitude, and often employ "minor" vigilantes and villains to help out with apprehending more significant ones: for example, recruiting Batwoman to help out with the criminals and vigilantes of Gotham. These recruitments are not always voluntary, and often involve some amount of cutting a deal or otherwise "incentivising" the asset in question. The DEO doesn't necessarily distinguish between criminals and vigilantes: regardless of whether or not Batman, Green Arrow, etc are "good guys", they are still breaking the law, and the DEO has a responsibility to enforce that.
In Gotham, the DEO field office is in the same building as STAR Labs: because of all the tech-themed vigilantes and villains in Gotham,
The DEO is not directly compromised by Checkmate (yet?), but they do answer to the Attorney General, who is on Checkmate's ruling council.
...DOMA?
If you are identified as a metahuman, the Department of Metahuman Affairs comes along to keep tabs on you. While the DEO are the ones who stop actual metahuman criminals, DOMA are the ones who provide counselling, medical treatment if you have complications from your condition, help if you end up out of work because of prejudices against your genetic problems, rehabilitation for those who resorted to crime as their "only option", etc. They're supposed to be friendly, helpful, and seen as a good thing... but because of prejudices, being a "registered metahuman" isn't that much better than being a registered sex offender as far as some people are concerned. Also, DOMA investigations can turn into a little bit of a witch hunt - though at least no one gets burned at the stake at the end.
...STAR Labs?
In our universe, STAR Labs is basically just another name for the National Laboratories (like Los Alamos, Fermilab, etc). It is a network of government-funded "Scientific and Technological Advanced Research" labs that has existed since the seventies, each with it's own different specialism / field of research. The lab in Central City is a particle accelerator, and also helps out the police with metahuman crimes. The lab in Star City focuses more on biomedical research. The lab in Gotham focuses on advanced tech and gadgetry. In Metropolis, the lab does a lot of research into Kryptonian physiology and that sort of thing. Mercury Labs (in Mercury, Nevada - near Area 51) does a lot of top secret research.
...Queen Consolidated?
Queen Consolidated is basically Apple. During the end of the 20th Century, Queen Industries was a pretty mediocre tech firm - their computers weren't quite as good as the PCs that Wayne Enterprises were making, their planes weren't quite as good as what Ferris Air was making, etc. When Robert Queen died however, his brother-in-law took over the company, and leached off Oliver Queen's "cool" status. They started focusing on making "fashionable" consumer electronics, starting with the QPid (iPod), and then the QPhone, the QPad, the QBook, all powered by the Qi ("key") operating system.
When Oliver Queen "died" (was stranded on an island), Glenmorgan started using his Checkmate connections to acquire other businesses, creating the Queen Consolidated conglomerate. Many of QC's early acquisitions were businesses already controlled by Checkmate (companies of former superheroes, etc), but quickly QC started going after villain/vigilante companies that were in foreclosure, and then branched out into hostile takeovers, gobbling up everything that might have useful research or patents, and merging them into a secret research division to make cool stuff for Checkmate's operatives and agents to use.
Queen Industries (Qi) still continues to make all of Queen Consolidated's consumer electronics, and is based in Star City. Quickstart Enterprises is like Google and Amazon had a baby: it makes internet TV, runs search engines (QuickSearch) and online retailers, there's probably QuickMaps instead of Google Maps, and all that sort of stuff. Stagg Industries is a petrochemical company that is constantly getting accused of shady stuff (think Shell Oil), but always manages to get away with it. They also own O'Shaughnessy's, a burger chain that is very popular in Star City / California / etc but is really hard to find anywhere else (basically In-N-Out); and Sundollar, a coffe chain that is literally everywhere (so, Starbucks).
QC also has Infinity, Inc which functions as it's research / innovation / think tank. On the surface, it develops new ideas and products for QC - things like electric cars, driverless cars, drones for Quickstart deliveries, etc. In the background, it's where all of the mysteriously disappeared companies that QC acquires ends up. Amertek Industries is a former weapons contractor that is currently experimenting with robotics and cybernetics. Cadmus Labs is a genetic research group that developed the Superboy clone for the military. Tyler Chemical is the company that developed the "Mirakuru" drug that gave Hourman his sixty minute powers, and is currently working on developing it into a viable supersoldier serum by mixing it with Venom, the Blockbuster serum, etc.
