Non Playable Factions
The Developer Team plans to include three categories of non playable (NP) factions.
Major Non Playable Factions
These factions - like the Cardassians, Ferengi, Eridians, or Hydrans for example - are fully intact small races. They usually have fewer vessels then a playable race and no avatars, but they have all that a player would need to control them - Starbases, Mining Stations, Yards, Support Ships and so on (a complete tech tree consisting of around 5-7 stations and 5-10 starships). They can also be found as completely intact AI forces on several maps. Usually major non playable factions have big roles within the Fleet Operations Universe. The Developers have some ideas in mind to let us interact with certain non playable factions (like the Cardassians for example) to gain specials from them, like a Galor for example. More details about that as soon as they are able to tell more, as these ideas only consist of sketches at the moment. As the developer team already announced something mercenary-like, you can be sure there will be ways beyond simple boarding to allow you to catch a few Galors and Hidekis.
Minor Non Playable Factions
Smaller factions - like the Orion Pirates, Maquis, Hirogen, Kazon, Malon, and Ferengi for example - do not have a full building spectrum. They usually have just a few key buildings which can appear on maps: like a Yard, a Trading Post or something of that sort. They will probably guard resources or something of the like.
A few “factions” do just consist of a single or a few units or structures, like Species 8472, the Crystalline Entity, a Tholian dilithium cracking facility and stuff like that. They usually will appear on maps with special events, like Fluidic Rifts etc. Map events are now possible, so if anybody comes up with some cool ideas they're welcome to post them in the official forum. The first cool stuff will be seen within the next patches.
Up and coming Non Playable Factions
In the Fleet Operations Universe the Tholians are no longer a major stellar power. They live in a handful of colonies spread across three solar systems. They have had an intact peace treaty with both the Federation and the Romulan Star Empire for more than three hundred years now and do trade here and there. However, because the Tholians are more "spiritual" creatures living in crystals with no exact material body, most of their trade goods are of no use to other species and likewise they do not need stuff like food, ale and spare parts. They are a cast-away and isolated race, happy with their peace and silence. Until one day...
The Tholians will play a large role in the Fleet Operation's storyline and thus will be featured as a major non playable faction. They will be able to access advanced and unique technologies, including special abilities which are similar to the Tholian Web in The Original Series.
The Cardassians will be able to build DS9-like stations (of course, they won't be called "DS9"). More information about the Cardassians can be found in the Dominion and Noxter sections, as they play important roles in the histories of these two other factions.