The key decision you will make throughout the game is what do you want to devote your empire's energies towards? Should it be colonizing new worlds, developing existing worlds, building larger battle fleets, or researching new technologies? By allocating funding towards these (and later on, more exotic) options, you map out exactly what sorts of actions your empire can take. Say for example that you have a large empire. If you devote all the empire's energies towards colonization, you could colonize 3 new worlds in a single space-month. Interstellar colonization is expensive! If on the other hand you devote all of your funds towards building new warships, you might be able to build 6 new space fleets. Warships are cheaper, but don't give you any income. Still, they're useful if you want to keep your neighbors in check.
You allocate funds to different options using the Economy Window (NEC picture). In this window you can see different funding bars, each of which represents one ministry of your empire. By left clicking on a funding bar, you can devote 1 point of funding to that ministry. At the end of each space-month, your funding will be translated into actual usable actions. Colonizing a world takes 2 points, so if you give 6 points of funding to the Colonization Ministry, at the end of the month you could colonize 3 new worlds. Building a space fleet takes only 1 point, so if you spent the funding on ship building instead of colonization, you could build new fleets around 6 of your worlds. You can de-fund a ministry by right clicking on it, or by left clicking on the new ministry that you prefer.
To use your accumulated funds, you can left click the icon for the appropriate ministry. So to colonize a new world, you would left click the Colonization icon next to the Colonization Ministry. At this point, every world you can colonize will be highlighted. Left clicking on one of these worlds will begin the colonization, and deduct the funds spent for that action. If you decide you don't want to colonize after all, you can either right click or press escape to cancel the action. You perform all of the ministry actions in this way.
Depending on how involved you want to get, and how much clicking you prefer, you can let the computer handle some aspects of administering your space empire. For instance, you can decide the level of funding for colonization, but let the computer decide which worlds to colonize. By left clicking the blue circle to the left of a funding bar, you allow the computer to take control of how to spend that funding. For colonization, the computer would try to colonize new worlds that have good future potential, and which are not too far from your existing worlds. In this way, you can either make all the decisions yourself, or reserve your human attention for the key high-level decisions. You can left click the automation circle a second time in order to turn off automation and resume manual control of that ministry.
Colonization and Development
Colonizing a new world settles several million of your citizens on that world, and claims the world and its resources for your empire. In addition, a colonized worlds acts as a fueling and refit station, and will expand the range at which you can launch new missions out into the galaxy. Colonization doesn't provide that much income though, at least on the galactic scale of things. Your colony can support itself, and act as a springboard for further growth, but that is it.
To gain serious income from a world, you will need to develop it, taking the planetary population from the millions to the billions. Developed worlds provide a great deal of income, and initially they will be your main source of funding. Developed worlds are also the only places that you can complete large projects, such as building a new fleet of space-battleships, or creating even massive orbital installations.
As a starfaring species, you have the technology to colonize most planet types. However, to truly thrive on a world and develop it further, your species will need to be naturally adapted to that planet type, or you will need to research new technology to grow on that planet type. Typically, an empire will only be able to develop 1-3 types of planets. This will be one of the defining characteristics of the empire, since it determines which worlds will be valuable to the empire and which will be relatively unimportant.
Once a world has been Developed, it has the industry needed to create enormous orbital projects that can alter the galactic balance of power. These projects range from rings of heavy star-forts, to enormous hab complexes that house billions, to massive arrays of FTL-enabled nuclear missiles. Each planet can only support two of these orbital projects, so plan wisely.
Fleets, Movement, and Combat
Happy space battleships are all alike, and are approximately equal in power. This means that as leader of your empire, your main concern for space combat is how many ships you have and where are they. You can order a fleet to move by left clicking on the fleet, and then right clicking on its destination planet. Your ships will move through space until they reach the destination. Your ships will then fire on any other fleets at that planet, so long as you are not at peace with the other fleet. Each of your ships has a small chance each instant to destroy a ship in an opposing fleet, and opposing fleets will fire on each other until one side or the other is destroyed. There is some randomness in combat, but generally speaking the larger fleet will win and will take fewer casualties. If you want to combine two small fleets into a larger fleet, you can left click one fleet to select it, and then right click on the other fleet to merge the two. If you want to split a fleet, you first select the fleet, then right click on the planet the fleet is orbiting.
If your ships are in orbit around an enemy world, and there are no defenders in orbit, your ships will begin to bombard the enemy colony. The more ships you have, the faster your fleet will clear out the enemy colony. If a colony is being bombarded, it cannot complete any development projects or new orbital projects. The only way to save the colony is to send a rescue fleet.
By default, all empires start out in a cold war with all other empires. Empire's in a cold war will not actively seek to invade or attack each other. However, if your ships are ever in orbit around the same planet they will fire on each other. (triggering a hot war NEC?). You can change a cold war into hot war by A) sending your fleets to another empire's planets, or B) angering an empire enough that they declare war on you. Alternatively, you can form a peace treaty with an empire by researching xeno-diplomacy, and then spending the funding needed to win the alien's trust. While in a peace treaty, empires will not fire on each others ships or planets. A peace treaty can be upgraded to an alliance, where both empires will fight together in any wars that they are in. However, you can only be in one alliance at a time. It is also possible to use the diplomacy techs to reach a ceasefire with an empire that you are war with. During the ceasefire, your ships will not fire at each other, and at the end of the treaty you will revert to a cold war relation. Note that each time you use diplomacy on another empire, your reputation for manipulation will increase, and future diplomatic actions will cost more.
The Escalation Meter is a measure of tension and fear between the empires. Escalation will increase as empires grow larger, wars are fought, and worlds are bombed into rubble. As fears increase, empires will be more willing to go to war in order to protect themselves against the threat of rival empires. The Escalation Meter will also rise when doom weapons are researched or deployed. Doom weapons are a class of weapons so powerful that they threaten all of civilization, and the mere existence of doom weapons will make empires more fearful of each other. When Escalation is low, empires will not use doom weapons, as they are simply too destructive and risky. However, if the Escalation rises high enough empires will become desperate enough to use any means to defend themselves against the other empires.
You can save up technology funding in order to purchase new technologies. Each of the technologies represents a major breakthrough for your empire, and will give your empire a significant new ability or a large upgrade to an existing ability. The technologies are expensive though, and you should not expect to research more than a half dozen or so in a single game. You should plan carefully how you want to develop your empire. Technologies take effect as soon as you spend the research points to purchase them.
Some technology projects are so dangerous that they have the potential to wipe out planets, stars, and empires. These technologies are collectively known as doom techs, and include things like planet shattering lasers, omni-vector plagues, and self-replicating autonomous warships. If you do decide to research a doom tech, you will be able to deploy the corresponding doom weapons at your planets. These doom weapon installations will lay in readiness, and can be used if the situation ever becomes truly dire. Because the destructive potential of these weapons is so appalling, they cannot be used unless the Escalation Meter is high. Each doom weapon has a special button at the top right of the screen; if you activate this button during a war, your doom weapons will be unleashed against your enemies worlds.
End of the game and Values
A game will end when there is only one empire left, or when the clock has run out for the game. At the end of the game you will see a short summary of how your empire fared, and what its fate will be in the coming age. Even if your empire was destroyed, it does not mean that you lost. Empires have Values which describe, well, what the Empire values. During the game your empire will receive points for acting according to its values. Some empires value trade and exploration, others value war and conquest, while other empires have values too alien and esoteric for the human mind to comprehend. In any case, how well you fulfilled your values will determine your score at the end of the game, and is good way to rank yourself against the other empires. Your score will also be useful for shaping the future course of your people, and can give new traits and abilities to your descendants.
The Galactic Cycle and Traits
After each game, one cycle ends and the next Galactic Cycle begins. Great empires will fall into decadence and fade, lost inside their own imaginarium. Their fleets will decay, and their doom weapons will grind to a halt. Stars will age, planets will evolve, and new stars will burst from the slowly collecting cosmic dust. In time, the refugees of destroyed empires will re-settle and rebuild, setting the stage for the next great cycle. At the start of the new age, you can take the experiences gained from the previous age and use them to shape your new empire. Each empire has Traits and Values, which determine what the empire can do and what it actions give it significance. At the start of a new game, you can use the points from your previous game to purchase new Traits and Values for your empire. You can also get rid of any old Traits or Values that you no longer care for. In this way, you can craft your empire over multiple games to best suit the story you want to tell.