Okay. While trying to explain City of Heroes to a coworker, I went over some of the main storylines of the game. Well. Some of them get kind of complex.
Now, this isn't a listing of all of the enemy groups. This is attempting to be a listing of the major storylines, and where those storylines stand as of Issue 12.
Nemesis - Current :
Nemesis is a reclusive genius bent on taking over the world. He does so because he honestly believes he can make the world a better place. At one point he was Emperor of America. He is noted for his advanced steam powered creations.
Nemesis also caused the Rikti invasion.
Nemesis - Ourobous :
Nemesis has succeeded in taking over the world at some point in the future. Something went screwy, and now he's trying to prevent himself from taking over the world... but not letting himself know that he's preventing himself from taking over the world.
If that confused you... don't worry. The general rule of thumb for CoH is that if there is no explination, it's a Nemesis Plot.
Nemesis also has his hands in the downfall of the 5th column and the rise of the Council through Ourobous.
Hamidon - Current :
George Hamidon loves the earth. He loves it a lot. There's just one slight problem. George Hamidon hates the humans. In fact he hates everything that isn't the earth. Now he's a big giant blob of sentient jelly that is literally eating his way through the earth to take control of landmasses and send his minions, the Devouring Earth, all over.
Hamidon has, at one point, developed the ability to turn humans into minions.
Malta - Current / completed :
The Malta are a goup comprised from members of the CIA and other secret agencies from years ago. Their aim is to control... everything really. They also work on building a giant super-hero killing robot. While the storyline is effectively completed, with the core of the Malta halted, there are hints that the Malta have some plots and plans up their sleeves.
Carnival - completed :
The Carnival is a group of mystics controlled by an ancient evil mask. The storyline is effectively completed, with explinations on the mask, it's powers, and how the Carnival came to be. However, it's widely presumed that the original mask has not yet been destroyed.
Rikti / The Lost - current :
The Rikti are from an alternate earth. Attacked by Nemesis they launched their own assault against the Heroes home dimension. The Rikti have appaerently captured and brainwashed Hero 1, and keep trying to shore up their positions in Paragon City.
The Rikti have perfected a method of turning an average Human into a rikti. The Lost, a low-level enemy faction, appears to be either Humans that are turning into Riktis, or Humans that have failed to turn into Rikti.
The Rikti themselves are split additionally by two factions. There is the Traditionalist faction, which is the small minority on earth, mostly made up of scientists and politicians. The Traditionalists are open to peace talks and a treaty, but have strict rules against non-Rikti. Basically there's a glass ceiling to the Traditionalist faction if one is transformed from human, into The Lost, into Rikti. While the Traditionalists hold power on the Rikti homeworld...
The Restructerist faction makes up the bulk of the Rikti on Earth, and they hold power in Paragon City. Driven by the Lord Of War Hro'Dtohz the Rikti they seek to conquer the planet, and occassionaly mass enough forces to invade parts of Paragon City they don't already have footholds in. Their only concern is getting enough portals back to their homeworld to bring in enough troops to crush earth once and for all. Various hints show that the Rikti Restructerists haven't been giving the full story of Earth's activities to the Rikti Homeworld.
They just have one... slight problem. Since they went after Nemesis's headquarters of operation first, their foothold just happens to be surrounded by one of the strongest superhero concentrations on the planet.
Another problem in the Rikti's plans is that as of Issue 12, a cure is available for The Lost.
Council / 5th Column
Another Nemesis plot story. The 5th Column is a Nazi-like organization headed up by a villain known as Requim. The Council is a similar organization headed up by a villain simply called The Center.
Early in the life of City of Heroes the Council overthrew the 5th Column and seized control. However, as found out later, the Ourobous collective was responsible for the overthrow of the 5th Column.
Currently there is a split between the Council and the 5th column soldiers. While the bulk of the Council follows the orders of The Center to the letter, the various generals inside the Council fight against each other on a regular basis. Many times the 5th council soldiers stay loyal to 5th council generals, resulting in what appears to be some nasty infighting.
The story seems to be getting more complex as Requim appears to have control over an Ouro Crystal of his own, and has been found to be time traveling. Various hints in the dialog indicates Requim has his eyes set on Atlantis.
Speculation presumes that there is a massive fight coming up as Requim and Nemesis go at each other threw time, and it's presumed that Requim will take up a direct fight against The Center in present time to overthrow the Council.
Circle of Thorns:
The Circle Of Thorns are... different. At first glance they are a mystical cult that specializes in summoning demons, offering sacrifices, and generally fitting the bill of mages gone wrong. However, the Circle of Thorns aren't... from the present. Their physical bodies are, but the minds and spirits of the Circle of Thorns are the minds and spirits of an ancient race, the denizens of Oranbega. The higher mages of the Circle of Thorns aren't just possessed by the spirits of old... they are completely made of the spirits of old.
Short version, the Circle of Thorns have mastered a power that allows them to store a person's mind and spirit in a crystal, and move it in and out of bodies almost at will.
The Circle of Thorns constant demon summoning and dark rituals provide a never-ending source of pain to both Heroes and Villains alike.
The quick shot on the Banished Pantheon is that they are the undead. The majority of their ranks are formed of zombies raised from the dead. They also feature multiple summons, and priests that wield superpowers.
Unlike most other villain groups, there is no central head to the Banished Pantheon. Rather, the heads of the Banished Pantheons are presumed to be Ancient Incarnates banished centuries ago. Where those incarnates were banished too, and how those incarnates can be brought back... hasn't been revealed in the storyline.
The Banished Pantheon's main impact on the storyline is the take-over of Dark Astoria, a section of Paragon City continously shrouded in a supernatural fog. It is presumed that the dark rituals of the Banished Pantheon cause this mystical fog.
Praetorians : Completed / Current
The Praetorians are much like the Rikti in being that they are both from an alternate earth. However, while the Rikti are from an alternate earth that is completely different in most physical aspects, the Praetorians are from a mirror dimension. In the Praetorian world the Heroes are villains, and the villains are heroes. Groups such as the Carnival of Light fight for what is good and lawful, while the corrupt twin of Statesman, the evil Tyrant, conquers all.
The Praetorian world is made all the more complex in that their are multiple dimensions of the Praetorian world, and multiple planets. In one Praetorian Dimension, the Council suceeded in taking over the world, becoming the Council Empire.
The Praetorian arc is largely completed, which players getting most of the in-game story wrapped up once they have a face down with Tyrant. However, the sheer number of hero / villain alts opens the Praetorian worlds up to future problems. As is now, nobody knows who, or what, Lord Recluse is over in the Praetorian World.
Lord Recluse / Arachnos
Lord Recluse wants to control the world. However, before he controls the world, he wants to take down Statesman first. There's nothing Lord Recluse wants more than to see Statesman on bended knee surrendering.
Storyline wise players face off against Arachnos at pretty much all levels. The spider forces even show up as low as Faultline. Currently one of the high-level TaskForces is dedicated to stopping one of the plans to take over the world.
The Arachnos storyline is further complicated in that like the Council, there is a lot of infighting among Arachnos forces, and even one of the top generals, the spooky Ghost Widow, isn't following Arachnos because she wants to. Not to mention the fact that another top general, Scirocco, only follows Arachnos because of a curse.
If you thought the above storylines were complex ... the shadow shard is even worse. In the Shadow Shard, an extra-dimensional plane (which also houses Pocket D) is filled with unending amounts of Rularuu forces.
There's also 3 demi-gods, consisting of Ruladak the Strong, Faathim the Kind, and Lanaru the Mad. Oh, and then there's the master of these 3, the so called Rularuu... which is never clarified as an actual entity, or extra-dimensional force, or another Incarnate.
The short version is, as learned in the Rikti Warzone, even the Vanguard is scared of what would happen if Rularuu were to be set free in Paragon City.
Okay. That's the list of the ongoing / not resolved storylines that I can think of.
There's also some on the villain side that aren't wrapped up by the time the players finish most of the story arcs in Ourobous.
And yes, I know that there are a lot of other minor arcs, like the Trolls Superdine, and the Family, and the Cage Consotorium not covered here.