Some blurbs from Wikipedia plus random musings:
The Hellsing Organization (more formally known as the Royal Order of Protestant Knights) is a fictional organization from the manga series Hellsing by Kouta Hirano.
It's a protestant order, in the Hellsing universe this causes plenty of friction with the Vatican and it's special divisions. Maybe you could work this angle if you decide to include similar organisations in your game.
The name "Hellsing" comes from the character of a similar name in Bram Stoker's Dracula, Abraham Van Helsing. The leader of Hellsing organization, Sir Integra Fairbrook Wingates Hellsing, is the great-granddaughter of the grizzled professor. In Hellsing's universe, the organization is an integral part of the true power-structure of Great Britain, which is in fact still ruled by a hidden aristocracy and the monarchy.
Like you mentioned before, this could be quite interesting for some political intrigue and the like if you and your players are interested in such a thing.
The organization is tasked with defending the country's shores from any and all supernatural threats. Controversy is often raised, especially in the manga, over the highly unconventional methods Hellsing chooses to do this, namely the use of anti-Christian powers and creatures.
Again, possible friction with the vatican if you decide to fight fire with fire (or in this case, the supernatural with the supernatural), possibly also with 'normal' military allies once they find out about your 'weapons'.
In the TV series, the agency's soldiers, uniforms, methods, and gear would suggest that it is a counter-terrorist paramilitary strike force.
So they would have all the latest and up to date equipment I guess
It is suggested that the Hellsing Organization was founded by Abraham Van Helsing shortly after the events of Bram Stoker's novel as a response to the threat posed by vampires after his encounter with Dracula. The purpose of the Hellsing Organization is to end all earthly activity of non-human creatures. It is traditionally headed by Abraham's descendants, as they are the only ones who can control Alucard, "the fruit of the Hellsing family's labors," whom they performed many experiments upon, building him into the ultimate undead for use in battle against other undead. In 1944, Arthur Hellsing, then the director of the organization, sent Alucard and a 14-year-old Walter C. Dornez to halt the attempts by Millennium to create an artificial vampire force that could help the Nazis win World War II. This they succeeded in doing, although they failed to kill the key members of Millennium. After WWII, it was decided that Alucard was too powerful, too potentially dangerous to be used as a weapon, and was locked away in the basement of the Hellsing mansion. Upon Arthur's death, his daughter, Integral Fairbrook Wingates Hellsing, became the director of the organization. Her uncle, Richard Hellsing, attempted to kill her and take the headship of the organization for himself, but was defeated by Alucard, whom Integra accidentally released from a 20-year internment, on instructions from her father. Integra herself fired the bullet that killed Richard. 10 years have passed since Integra took control of Hellsing.
Some general background info, also begs the question, how far are the PC's willing to go to stop the Nazi experiments, will they use whatever means necesary or do they have reservations about certain (more extreme) methods?
The Iscariot Organization, named after Judas Iscariot, the apostle who betrayed Jesus, is a top-secret wing of the Vatican (the section that's not supposed to exist) charged with the active pursuit and extermination of demons (such as vampires) and heretics. Given that the Hellsing Organization not only employs vampires but is run on the principles of staunch Protestantism, Iscariot is their natural rival, despite their similar aims.
Like I said, plenty of friction with the Hellsing organisation, so if you include similar organisations in your world, there's no guaranteeing they'll be allies at all.
The Iscariot 'paladins' are the elite fighting force of the Iscariot Organization. They appear wearing long cassocks and crosses, in the manner of their most prominent member, Alexander Anderson. They are known to fight with a wide variety of weapons, usually as necessitated by the situation (for example, Alexander Anderson wields blessed bayonets that are especially effective against vampires, while Heinkel Wolfe is armed with simple pistols, effective against her human targets). The Vatican's Special Section XIII also commands other seemingly independent military forces, most notably the Knights of the Sagely Brethren, the Knights of the Order of Calatrava La Nueva, the Knights of the Military Order of St. Stefano di Toscana, and the Knights of the Order of Malta.
Plenty of ideas for underground Vatican organisations and the like, methinks, should open up a whole new world really, especially since they don't always play nice or by the book or anything, even though for a large part they consist of clergy
In addition to Iscariot, there is another special section of the Vatican; Section III Matthew, named after St. Matthew. In Hellsing, its purpose is the retrieval of various holy relics and artifacts. This is in accordance with its name, "Matthew," which is derived from the Aramaic name "Mathai," meaning "Gift of God". They were the ones that 'acquired' Helena's Nail, and gave it to Iscariot, who bestowed it upon Alexander Anderson for use in battle against Hellsing's vampire, Alucard.
If Matthew is Section III, and Iscariot is Section XIII, then it is probably safe to assume that there are eleven other sections of the Vatican, each of them named after an apostle of Jesus, and each of them existing with a different purpose.
Plenty of room to customize them into different niches like you already talked about earlier on. Also makes for some fun and diverse encounters seeing as no two sections will be the same, so the players might be in for a surprise. You can give each section it's own 'feel' and preferred equipment and modus operandi and what not.
Little is known about the history of the Iscariot Organization. However, it is revealed by various characters that Iscariot has existed for a long time, possibly as long as Christianity itself. The existence of Alexander Anderson suggests that Iscariot has perhaps engaged in genetic engineering and other advanced technologies to fulfill its purpose and to create greater weapons with which to combat its enemies. Iscariot has a sacred duty to do battle with the "seven million, four hundred and five thousand, nine hundred and twenty-six demons of hell".
As you can see, holy organisations also have their own 'evils' to battle evil, I mean, a vatican organisation using genetic engineering and what not? I guess they're willing to do whatever it takes to accomplish there goal.
Iscariot also has a bitter rivalry with Hellsing, due to their differing ideologies. Hellsing is an Anglican organization, Iscariot is a fundamentalist Roman Catholic organization. Also, it is implied that Hellsing kills vampires because of what they "do". Hellsing will not attack a vampire unless it poses a threat to the Church of England or to the British Crown. Iscariot, on the other hand, kills vampires because of what they "are".
Different viewpoints can cause plenty of friction, again enough RP and background options if you decide to use different organisations in your game
A paladin, or warrior priest, who works for the Iscariot Organization. Like Hellsing's Alucard, Anderson is Iscariot's trump card, except that he is a human, rather than a vampire. However, Iscariot has enhanced Anderson through some kind of genetic engineering, turning him into a being known as a Regenerator. His mission (both personal and professional) is the destruction of all of Hell's demons, including Hellsing and Millennium. To complete this mission, he uses his arsenal of blessed bayonets and sometimes his bare hands. He is Alucard's main rival and adversary.
Like I said before, this guy takes the word 'zealous' to a whole new level. Once he get's going there's nothing that can stop him, not even orders from higher hand in a lot of cases, all the while quoting bible passages. He really is a religious fanatic, also with a stern hate of protestants.
Enrico Maxwell is the overzealous leader of the Iscariot Organization.
Typical power hungry megalomaniac, 'nuff said
Hope some of these blurps can be useful for inspiration