We're over eight games into the X series, and X's sci-fi world doesn't feel all that fleshed out. (The classic series in contrast is more like our world, so it gets more of a pass.) Plus fighting Sigma's goons every game's getting boring. So what other kinds of organizations besides the Maverick Hunters and Sigma's Mavericks probably exist in X's world?
In general, these are the kinds of newly introduced organizations we could see the Maverick Hunters interact with:
1) Mafia
There is definitely organized crime among Reploids. If they were to be classified, I think they would come in four varieties:
a) Mafia that targets Reploids only.
b) Mafia targets both humans and Reploids.
c) Mafia that's pro-Reploid and opposed to viral Mavericks like Sigma.
d) Mafia that's pro-Reploid and in league with viral Mavericks like Sigma.
We already know that type d exist, but they're boring because they're just a front for Sigma. Out of all of these, I think a and c are the most interesting to me, although type b is only slightly less so. Type a is interesting because they are not posing a threat to humans, and therefore such an organization may not technically be Maverick legally speaking, especially if they use disreputable but legal means to achieve their ends. Type c is interesting because there are probably many supporters of the Maverick cause who are absolutely opposed to Sigma and viral Mavericks. Why side with crazy and infected people and risk getting infected themselves, especially when Sigma's schemes started getting really destructive? Instead, why not focus upon subverting the system on their own? They also may be able to find common cause with the Maverick Hunters sometimes, as terrorism and viral outbreaks are bad for business.
2) Revolutionary/Reactionary organizations/corporations
These kinds of organizations probably also come in a few varieties:
a) Pro-human and anti-Reploid, and only consisting of humans.
b) Pro-human and anti-Reploid, but including Reploids in their ranks.
c) Pro-Reploid and genocidal against humans but against viral Mavericks.
d) Pro-Reploid and anti-human and in league with viral Mavericks.
e) Pro-Reploid and anti-human and dominating of humans.
f) Pro-Reploid but not anti-human.
g) Neither pro-human nor pro-Reploid but opposed to the government.
Type a showed up in the Archie Comics in the form of the Emerald Spears, but as expected they're laughably weak. It isn't until much later in the time-line such as near the end of the Maverick Wars and during the Elf Wars that humans are able to develop technologies, such as Cyber-Elves and full cyborgization, that allow them to effectively combat the Reploids. Type a could work earlier in the time-line, but it would need Iron Man / Samus Aran -like exosuit human soldiers, or they would have to develop some other type of robotic beings analogous to Reploids, or some combination of the above.
Type b could be seen as a more extreme version of the Maverick Hunters, not unlike Red Alert but more organized and including tons of human members. The military would probably be the most fitting possibility for type b, especially after the fall of Repliforce showed the danger of having an all-Reploid military.
Type c and type e are both pretty interesting, and it's unfortunate we haven't seen many organizations like this so far even though I imagine they'd be pretty common in X's world. Type d is boring at this point and we've gotten at least three flavors of this already with Sigma, Gate, AND Dr. Doppler, with Gate being the least anti-human, Doppler being the most pro-Reploid, and Sigma being the most anti-human and the most genocidal. Type f has also already been appeared before in the form of both Repliforce and the Rebellion Army.
The Resistance in the Zero series is a righteous example of type g, but there are probably many more morally dubious organizations of type g in the X series. The goals of type g organizations could either be to replace the government, making them a more well-meaning version of type e if the new government is run by Reploids, or they could just be anarchical organizations.
Anyway these are the kinds of organizations I could see existing in X's world. I dunno what do you all think? I'm sure these kinds of organizations have shown up in fan-fiction before, but it'd be nice to see more of them in official games especially as a change of pace from the constant battles against with viral Mavericks especially Sigma and his subordinates.