1)Factions:
In Star Trek: New Frontier. You may choose from several major factions that are always seen interacting with one another, fighting with each other, or just fighting someone. The four different Factions to choose from in this Guild are as follows:
1) Federation
2) Klingons
3) Romulans
4) Independent
The Federation, Klingons, and Romulans have their own starting amount of credits, ships, upgrades, and more that are only purchasable by members of their own faction. This allows you to easily manage your ship if you want to upgrade it. The more credits you have, the bigger of the ship you can buy, the stronger weapons you can buy, and better upgrades you can buy.
If you choose Independent as a faction, you forfeit some abilities, but gain others too. Although you cannot buy the more powerful ships, weapons, and upgrades, you can mix and match any available upgrades from any of the factions, creating a truly powerful and devastating ship customized to fit your own needs.
When choosing your faction, be careful, you cannot change (in most cases). Also, be aware that if you join a certain faction, you may find yourself fighting one of the others or allying yourself with another. Not to mention that you may become outnumbered and outgunned if your enemy brings in bigger and better guns. Just remember, you always have warp, and even if you don't, backup is only a distress call away...
As a little addition, I'd like to clarify something about factions. While usually you can't change factions, some NPC-type characters may offer you the chance to work for them, allowing you to change your alliance. However, this can only be done if you are actively engaged in the main storyline, or happen to come across them in the RP. This opens up all kinds of new possibilities for one to expand on their role-playing fun!