A generation ship is a perfect ant-farm where different societies can coexist within a limited space, influencing and affecting each others' development while fighting for that limited space, which adds “the end justifies the means” pressure. Let’s take a look at the various factions and groups:
Protectors of the mission
The Protectors' one truth is the Mission, and the sole way to ensure successful completion of the Mission is to follow the Old Ways. The ways of the fathers, forefathers, and Founding Fathers are together the beam upon which the Ship travels to our ultimate destination. The mutiny, which through their steadfast and timely intervention was thankfully aborted, was the ultimate betrayal of the Old Ways, of everyone who had come before, the nullification of every sacrifice and every life dedicated to the Mission.
Sworn to regain control of the Ship, the Protectors will subjugate anyone who threatens the Mission. Over the last century they have managed to expand their enclave somewhat, but the Brotherhood is deeply entrenched. To overcome them with violence would result in a massive loss of life, an unfortunate consequence which itself would endanger the Mission.
The Protectors are governed by the Mission Control Council, which appoints the Mission Commander to implement their policies and decisions. Failure is regarded as a deviation from the Mission. As such, Commanders are twice as susceptible to death-by-misadventure as the average citizen.
The Brotherhood of liberty
The Brotherhood was formed to liberate the people from the iron shackles of the Ship Authority. Though their first sally -which the fossils of the old world denigrate with the term "mutiny"- failed to completely achieve this aim, the Brotherhood was successful in establishing themselves as a power to be reckoned with. More importantly, their ideals of liberty and freedom are now discussed everywhere.
The Brotherhood's initially pure goal, to free the enslaved wherever they may be, has unfortunately been sullied by the practical concerns of democracy. If the Brotherhood had had access to the older histories they would have realized that democracies beget their own factions, factions which cannot be put down with violence for now they are within. The Executive Council was also forced to consider issues like the right to vote, and whether it should be granted freely to all, or earned through service to the state. The first generation earned their rights rebelling against the tyrants, whereas the youth of today have forgotten even the names of those heroes. Easily swayed by rhetoric and bribed with cheap comforts, these layabouts could hardly be less concerned with such abstractions as liberty and universal suffrage.
To bring freedom to the Ship entire must involve war, and no war may be won without sacrifice, nor may battles be managed by committee. The unwillingness to back high ideals with bloodshed is, as far as the Council is concerned, the reason for the recent losses against the Protectors. Yet any attempt to limit majority rule must be interpreted as a retreat from the ideals upon which the Brotherhood's very identity is based.
If every decision, even those which mean death to some of the Brotherhood's own citizens, must first be approved by a majority, how is it possible even to start?
The Church of elect
As inevitably happens in dark and challenging times, some citizens turn to God for reassurance, the promise of an end to pain and hunger. Or failing an end, at least a purpose.
The Church of the Elect rejected both the Protectors of the Mission and the Brotherhood of Liberty as worldly fools distracted by politics and their own egos. Teaching their adherents that they were chosen by God, the Church frames the journey of the Ship as a centuries-long test of faith. We all face a series of difficult trials, yes, but with a very definite end.
When the Ship arrives at her destination, Judgement Day awaits every citizen. The righteous will be welcomed into the Promised Land of Alpha Centauri-4, while the unrepentant will be returned to the Hell from which we fled -Earth- to suffer for all eternity.
Led by the Chaplain-General, the Church of the Elect is a militant organization. While Christ was undoubtedly a man of peace, what he preached on Earth does not strictly apply in the void of space. Extraordinary challenges require exceptional measures, for even Jesus can't do much for an unarmed man.
Men of the covenant
When a small percentage of children in the Habitat were first born deformed, they were immediately shunned. Superstitions – that their deformities were contagious, that they were radioactive – swiftly followed and they were branded Mutants. The young were abandoned, and those whose defects didn't manifest until later driven out of the Habitat.
As the number of outcast Mutants grew, they began to settle in what had come to be known as the Engine Room, the vast open space providing access to the Ship’s engines and reactor. With the condition of the fusion reactor degrading to dangerous levels, and the number of volunteers for jobs in areas exposed to radiation remaining few, the Mutants approached the Habitat to negotiate the Covenant, a pact granting the Mutants protection from harassment and violence in exchange for their maintenance of the engines and other vital ship systems.
Out of necessity, engine work and electronics were taught to the outcasts by Engineering Officers, and out of "charity" Christianity was introduced by the missionaries. Over the decades, the isolated Mutant collective became increasingly tribal, and the confused worship of both science and religion led to a theocratic, caste-based society. Believing themselves chosen by a higher power, the Mutants declared their disfigurements not a curse but the Mark of God, the physical manifestation of their destiny to save the ship, and thus mankind.
Now the Mutant priests hide the stigmata of their kind behind masks depicting beatific metal faces, and their Consecrators regularly tour the Habitats, to seek out children bearing the Mark and to spread the word of God. Frowning upon (or more aptly, fearing) such blasphemy, the Church of the Elect claims that the Mark of the Beast is the proper name for the Mutants' affliction, but as long as they tend the Ship's engines they remain inviolable.
At the heart of the Ship sits one of its deepest mysteries: the House Ecclesiastes. A simple, unadorned facade belies the importance of this temple, and the curious visitor is welcomed by nothing more than a centuries-faded relief spelling ECLSS and two well-maintained turrets. Only senior faction representatives are granted audience here. All others are turned away.
The monks of House Ecclesiastes are the keepers of many secrets. Deep within the zone, they are said to meditate on the very essence of Life and Death, but their practice is not one of philosophy. Their rituals are crucial to the systems that allow every citizen to survive. The burden of their knowledge is so heavy that they have cast aside all other earthly concerns, caring not for wealth, pleasure or power. Thus their motto: He who increases in Knowledge increases in Sorrow.
With few exceptions the needs of these ascetics are modest, but whatever they request, they promptly receive. In return they offer nothing but the continued supply of air to breathe and water to drink.
Generations will come and go, but the Ship is eternal.
Recognizing neither the Protectors of the Mission or the Brotherhood of Liberty, the Freemen submit to no one's laws. These ruffians have no respect for titles, tradition, or any rules restricting their right to live in whatever manner they choose.
Refusing to trade their principles for the comfort and safety -and the subjugation that goes along with them- of the various squabbling boot-licks of the Habitat, the Freemen have chosen to settle beyond its borders, where they make a living as scavengers, traders, and highwaymen.
The center of their domain is one of the Ship's capacious cargo holds, now a container town. Aptly named The Pit, it is dark, cold, and lawless, a place where a person might go to secure an illegally modified pistol, or a flask of alcohol fermented in a disused cooling duct, and end up with a blade in the gut instead. As the Pit offers nothing of value to either the Protectors or the Brotherhood, it currently enjoys all the freedoms a citizen could desire.
But however much the Freemen shout about their ideals, should the situation change these anarchists may find themselves truly liberated — from all worldly laws and cares.
Rumor has it that Captain Braxton once served a higher power, that in the days before his crisis of faith and the subsequent falling out with the Church of the Elect he was known as Faithful Gunner Jeremiah Braxton. Speculation about why he left is abundant, but as is often the case no story is more compelling than the others.
Backed up by a few like-minded men and picking up more willing recruits along the way, Braxton left the Church behind and ended up in the Pit, a place where reliable fighting men are always in demand. Around the time of his arrival, the Brotherhood had started showing a keen interest in the Pit, eager to establish a foothold there.
Braxton and his newly christened Regulators offered the good people of the Pit their services and after much debate they were hired to drive the Brotherhood’s men out, which was accomplished with brutal efficiency.
With a belief system consisting of a chaotic mishmash of tradition, the teachings of Jesus Christ, and an an anarchic hatred of authority, Jackson's Riflemen make a perfect ally for exactly no one. But what they lack in congeniality, they make up in firepower. The Riflemen control the Shuttle Bay, a fully outfitted, Earth-tech maintenance and repair facility, which allows them to produce professionally machined guns for trade and their own defense. They've also managed to restore a couple of pre-Mutiny riot droids and equipped them with heavy machine guns to deter uninvited guests.
You start the game as one of the Freemen who grew up in the Pit and thus have limited knowledge of the Habitat. So when you travel there for the first time, you'll be a stranger and have good reasons to explore the factions and their beliefs in how to make the
world ship a better place.