
Does this have to be a FPS?
I would much rather play this from an isometric point of view. Get in a little bit of the MGS feeling. If you''ve ever played the game Crusader: No Regret (and its predecessor) by Origin, I thought that game had a good balance between tactical espionage and all out gun fights. I also thought that MGS2 was very sloppy in the way it handled gun-fights.
However, that is not what you wanterd help with
You could expand your story design further like this:
These two alien races are battling over a rescource which is in somewhat high demand (and short supply). Let us say that it is a form of quark ''soup'' which contains lattices of sub-atomic particles which have ''traction'' on the sub-space energy grid, so when energized, this substance can create extra volumes of containment, micro-vortices that can be used to hide anything up to entire planets, and at peak input, these lattices can be used to wormhole through vast quantities of space. The unfortunate news is that these lattices decay at an alarming rate when energized.
This is relevant because one of the inner planets in the home system of the smaller of the two races (race B?) is home to a phenomenon which seems to create the stuff, and eject random streams of it into space.
A prominent method of transportation is creating short range (up to 15 light-years) displacement volumes. This can be carried out using what is considered to be standardized equipment by most space-faring races. However, the quark-lattices allow for a very comfortable 300 to 500 light-years of instantaneous travel, because of this, these lattices are very much sought after.
To begin with, I may assume that the player character will be a mercenary from a third party race, because the conflict being overseen in the game (as I envision it) is purely between two races who want to control something, but are at a stand-off. For this reason, I think that all civilians should not even know of the existence of the quark lattices, and it should not be common knowledge among scientists of any race.
The phenomenon that is creating the lattices is a temporary infusion into the current universe from a higher order universe (a parallel universe that is older than ours, and hence it is closer to destruction). It is entirely conscious of its own existence, and it has a strength of influence over its surrounding space so strong that it is perfectly aware of the conflict that surrounds its presence. The lattices it ejects are a by-product of its construction (it is a bridge between universes, it is still under construciton, but once that process is complete it will stop ejecting lattices and turn into an actual gateway through which another much more advanced race will enter this universe.
The two warring races established a space station called the Cauldron of Light some hundred years ago, in which members of both races live. When Race B discovered the anomaly, they attempted to harvest the substance as best they could. Race A however, had spy satelites around, and when they detected the increased activity sent scout ships to investigate. In the beginning all was well, until the warrior caste of Race B decided that it was in the interest of their race''s progress to stem the harvest of this stuff by Race A.
Race A was not happy, but did not expect to have much trouble implementing a diplomatic solution that would allow them to continue to harvest half of what was present. The warrior Caste of Race B didn''t like this solution so they declared war on Race A and garrisoned a section of Cauldron of Light along with constructing a strategic defense network around their home system which would prevent Race A from getting near it.
The player may have been asked by race B to join in a covert infiltration mission which required them to gain control of certain parts of the Cauldron of Light
At this point most of what Mr. AP said comes in. I would add that the religious caste of Race B is trying to get through to Race A delegates.
I would say that the religious caste of Race B definately wants an end to the war, and Race A never wanted it anyway, but despite their larger numbers they are suddenly having to deal with offensive vehicles coming in from all sides because Race B is tapping this new rescource for all it''s worth.
I would leave most of the pivotal decisions up to the player, but I think that if a time comes when Race B has clearly secured the continuation of the war, the phenomenon will begin teleporting the strange lattices out of range of retrieval (say about one million light-years away). Obviously, this means that what Race B sees is that the source just stopped producing. They will subsequently realise that they have spent all of what they harvested in the war efforts.
The player should then recieve a message from the warrior caste, and another from the religious caste, because the news got out of the dubious moral high-ground that the war was based on. Each message asks that the player return to their home system and fight for that side in an attempt to restore order (basically the religious caste wants to oust the warrior caste). If he replies positively to either one, that side will offer transportation and other services to get the player to the battlefield.
If he replies negatively to both, The warrior caste wins. They begin an all out assault against Race A (which is somewhat weakened, so the two races are approximately on equal terms). Race A reciprocates, and things get hairy (I leave it up to you what the player does for this time). Some ten years later the gateway finishes itself and the new race comes along and attempts peaceful contact with Race B, unless the warrior caste has been overthrown Race B will get its ass whooped because it thinks this is an unwarranted invasion into their own space.
Then, the rest of the races have a very angry bull in their back-yard

A quick side note: I would like this to be divided into two games, the first dealing with the conflict up until the end of the war on the Cauldron of Light. At some point, there should be a scientist or researcher somewhere on the station who talks about how strange the anomaly is and how it sometimes acts like it''s alive (just as a pre-implication of things to come in the second game). The second game should start with the internal conflict of Race B OR the continuing conflict between race B and Race A, and should end soon after the gate is completed and the new race comes along, (and potentially starts a war that cannot be won by our races).

Are you in support of the ban of Dihydrogen Monoxide? You should be!