One idea I had last night was to put the whole story into the frame of an alien conspiracy and limit the war between worlds to a struggle between two "secret services": One human and one alien secret service.
Human-Phalanx versus Alien-"Phalanx"?
On one side we have the Phalanx, on the other hand we have the Alien "Elite Forces", trying to implement a secret agenda assigned to them by their leaders. Thus we avoid a setting in which a big war between worlds is going on. Instead we find ourselves as part of a struggle between secret services. This will allow us the eliminate the David vs Goliath situation that has been subject to critique before. (I remember some people saying that it sounds unrealistic that a tiny little force has to fight against an invasion of huge alien forces.)
The Secret Agenda of the Aliens
So what is the secret agenda of the alien secret service? They are assigned to carry out certain mission (the installation of sophisticated devices) that result in a climatic change on earth. This climatic change will turn our planet into one that provides ideal conditions for their own race. As a side effect the human race and other earthly species will be eliminated. The idea is simple: They don't need to carry out a real war. If they succed to set up the mechanism that creates the climatic change, they can change the "grammar of civilizations" and get rid of rival species over time.
But they have to carry out this plan carefully. In order to prevent suspicion to raise amongst humans, they aim to "stage" this climatic change as an "approaching Judgement Day". They want to exploit religious belief in order to camuflage their endeavour. This will keep any conscious resistance at a minimum. In short, while the aliens deploy their devices, they also use other smaller devices to cause a number of natural disasters to hit the globe. Some magazines and channels already broadcast programs that interpret these disasters as the sign of an approaching Judgement Day and refer the religious texts. Public Opinion shifts more and more towards a metaphysical or religious explanation of the row of disasters.
On the other hand, some nations seem to have gained access to certain technologies that they are normally not capable of to produce. It appears that some of these nations start to put a distance between themselves and Sector 911, eventually resulting in withdrawal from the organisation and followed by hostile actions towards 911 agents.
What is tbe objective of the Alien Special Forces? Their objective is to set up a number of gravitational devices on earth and on the moon which will fix the moons position in such a way that it results into a constant eclipse of the sun. This will cool down earth as a whole, starting a new ice age, creating famine and leaving only a few humans alive... only a bunch of humans survive, which can be exterminated easily once the colonization of the "new and comfortable home" has started. On the other hand they install some devices that cause natural disasters... so that the shift in the moons behavior is related with the idea that Judgement Day has come. All this causes a stronger interest into religion and metaphysical explanation of the situation. Organization like the Vatican think their time to rule has come and they contribute a lot in making the "Judgement Day has come" idea even more popular.
In order to "work" comfortable, the aliens seek for allies around the globe. They contact leaders and bureaucrats, infiltrate institutions and services in order to gather intel and other support. They bribe or brainwash agents in order to make these services or nations to act in favor of their agenda. This is dangerous for the Phalanx, because a growing secret alliance between pro-alien nations and secret services means that Sector 911 weakens. These nations start to regard the Phalanx as an enemy and deny its access to their territories. They also deny the trade of unique products and services of their nations. Finally they dare to attack our HQ and other buildings.
Our goal as the commander of Phalanx is to gradually find out about these evil goals and objectives, and eventually, to defeat all enemies.
The Phalanx
But who is the Phalanx? It is a special research unit founded under control of the CIA during the increase in "flying saucer" incidents in the 1950s. Its goal is defined as "conducting research on extra-terrestial life forms in order to prepare the earth for a possible encounter with the "third kind"". It is a a group of experts coming from fields like computer engineering, Physics, Chemistry, Genetics, Biology etc... They search for evidence of other forms of life by making tests on everything that is believed to some extend being of extra-terrestrial origin. They also do research on rocks and stones brought from other planets or on asteriods that hit the earth.
After 9/11, the worlds secret services, led by the USA, decided to fight Terrorrism on a global scale and established a Global Intelligence Service, also knows as "Sector 911". Sector 911 was an umbrella organization that combined the databases and resources of almost all the secret services of the world in order to maintain global intelligence and to conduct counter-strike activities against enemies. In 2027 a report titled "The Possibility of Extra-Terrestial Terror" resulted in fear and paranoia amongst the leaders of "Sector 911". They decided to set up a unit that would prepare for a fight against such Extra-Terrestrial Terror. As a solution, they came up with the idea to integrate Phalanx into "Sector 911" and give a Elite Force into its command.
The Phalanx is now a special research organization that enjoys the comfort of making use of the resources, technology, funds and intel of a global intelligence service. It also enjoys having its own Elite Forces. However, the paranoia of Sector 911 leaders never proofed to be true and until today, the Phalanx Elite Forces never had an encounter with the Third Kind in any of the missions they were assigned to.
But that, my friends, will change soon :-)