Beings and species which cannot be reasoned with or negotiated with. They must end especially if they have already repeatedly drawn first blood. This must be done in order to save the lives of those who only desire peace.
The best idea is to find remote locations within a galaxy. Which is limited of any energy resources. Also, which causes long travel and the exhausting of stored energies within any known class of ship. Assuming the technology is at such a level that free energy creation is still improbable and that absorbing energy from stars is the preferred method. Maybe even a technologically stagnant preferred method.
1). Create, build and manage your own star or star's. Or by locating a stable binary or triple star system. Would prove beneficial as one could be used as a energy source while building and energizing the Dyson Sphere.
2). Then beginning in the habitable zone. Begin building the inner perimeter of the Dyson Sphere. Consider our own star and Earth. The inner perimeter would begin somewhere between the orbits of Venus and Mars. From the inner perimeter to the exterior perimeter of the actual Dyson Sphere can be many tens of thousands of miles thick. This must support both the interior and exterior mass.
3). Begin collecting preferred natural minerals. Even if you have to travel many hundreds of light years in all directions. Then place them inside along the inner perimeter. Creating a habitable area for all life you choose to inhabit the inner all light area. This is more about strategy than technology to create or program your own minerals and compounds. The planet like minerals can be up to or more than many thousands of miles thick.
4). Once the inner portion of the Dyson sphere is complete. Begin adding life into the inner zones. From smallest to largest. All life which can thrive in an always light environment.
5). The outer portion or exterior perimeter of the Dyson Sphere should be lined with a variety of major offensive and defensive weapons systems. I'm a believer that you cannot have to many guns. Especially, when your at war with those who cannot be reasoned with or just refuse to consider any other course of action.
6). The outer portion of the Dyson Sphere should contain many thousands of miles deep with salt water ocean ice. The weapons platforms should extend beyond the ice.
7). The whole engineering process is completed when the entire Dyson Sphere acts as a gyroscope. When all life within is self sustaining. All weapons platforms can store their individual energies and be able to quickly repeat fire many hundreds of times.
8). The programming of atoms and aligning of atoms must be a technology which is easy for those to use however they desire or decide. Which means the robotic machines used to create the actual structure of the Dyson Sphere can be made of a metal whose atomic structures are aligned and in close proximity to one another.
9). The creation of robotic systems to build, maintain and defend the entire aspect of the sphere. The robotic systems should be capable of networking and team work. This should already be happening for some time. There should be many hundreds of trillions of these robotic machines in the creation process. Then once their service is complete or there is a problem. They are energetically assimilated back into the system and re-created into something which is needed. Or recreated into offensive and defensive robotic machines which goes forth to ascertain an enemy and allow passage or destroy them all.
10). The amount of life which can be sustained could measure in the many hundreds of trillions. Including human life. That would be only on the inner surface of the Dyson Sphere. This does not include the population of the Dyson Sphere machine itself.
11). Then it can move. Thus, not being able to be located or found. It should also have the ability to absorb energy from any star it interacts with. Thus, capable of removing all of its own fuel. Their enemy will be able to extrapolate when stars just blink out and planets begin to roam free.
12). Used as an offensive weapon. By hoping into the central portions of any solar system and absorbing the energy from those stars. Or causing those stars to become destabilized to the point of explosion. You will deny energy for the enemies warships. Then abide your time and destroy them all. There is also energies within every planet. So any planet inhabited by the enemy. Those energies should also be absorbed. Just like the great Nazi WW2 Battleship which left port alone and suffered it's final fate at the hands of lesser warships and planes. There should be more than one of these huge Dyson spheres. To work, support and fight together. To go it alone. Is not a wise strategy.
13). Locating lesser species who have the determined capability to make a leap from their current state of lesser technology to your state of technology would be a wise find. Especially, if their population has become numerous. Thus, guiding willing souls to achieve more than they were would go a long way to save you all. Any reasonable lesser species who learn of a coming threat. Should make the wise decisions on their own to some degree. assuming there is time and if there is no time. Then those lesser species should be invited into your great ship.
14). Rotational engineering of the Dyson Sphere. The mechanical structure of the Dyson sphere should be able to self rotate as part of an uncertain and ongoing strategy. The internal and life supporting part of the structure should have it's own rotation. The exterior of the mechanical structure of the Dyson should also be able to independently rotate in any particular direction not associated with the internal perimeter of the structure.
===Throwing Rocks is just rude.===
Even today in modern US Military practice. When they build a fortress. They love to clear out a lot of land. So as to prevent hiding places for snipers and other bad guys. This is why you would need to clear out everything within 100+ light years(estimate). Which includes anything which emits any sort of energy or resource. So that when an armada of ships comes within range. They will have no opportunity to absorb any energy from a star. To energy means no use of weapons systems or the ability to maneuver. One of the aspects of the defeat of WW2 Germany was their inability to procure fuel. Thus their tanks and planes could not be used.
Back to clearing out everything. Which also means all asteroids, rocks and planets. Even down to minute particles. Once a species has the ability to absorb energy from every star. Then it would make sense that they can also create stars and planets. Which you could also assume that they can also move those objects into their pre-planned orbits. Which means they could begin throwing asteroids at your ships or planets.
Think about our solar system. Us human beings on this one little planet is literally surrounded by an asteroid belt as well as the Oort cloud. We are basically in a very bad situation as any species who can and have their own ability to travel from one star to the next star with a very high probability of not experiencing any accidents. Then they would have the ability to throw asteroids and comets at Earth at any time. Even sending them on long orbits to strike a specific place at an exact time on the Earth sometime in the future of their own choosing.
Possible Reality: (Unedited): 26 May 2017:
Added on 27 May 2017:
No matter how advanced or superior you seem to be to the majority of life forms. Surviving a threat from an unreasonable and unnumbered foe which is seemingly superior to you. Will require you to take those impossible leaps into the realms of probability and possibility. Yes, to cause you to choose to step away from certainty. Which as of yet not even conceived by any of your own people as of yet. You may even need to suck on that sour pill of forgotten humility and seek guidance and education from those insignificant species whom you may have abused many many millennia ago. Which may even now have been forgotten by them all. I would bet they would even accept your return.
To avert all of the coming bad and sad prophecies. We each must decide to do the following everyday, every hour, every minute and every second.
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