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Let’s start with our design goals:

Mutants are a time-honored staple of the generation ship genre, plus it’s an opportunity to do something interesting and add a radically different faction to the three ‘grounded in reality’ factions (totalitarianism, revolutionary democracy, theocracy) controlling the Ship.

The mutants should be viewed as abominations by some (meaning they should look ‘different’), yet still considered humans by more open-minded folks, meaning the mutants aren’t the hulking brutes of Fallout or the over the top two-headed, three-armed mutants of The Orphans of the Sky.

Thus when it comes to design, we’ll use the human model (making the grateful animator’s life much easier), which means that all we have to work with are the portrait and ‘accessories’, which limits our options.

Overall, the mutants aren’t monsters to kill but a forced evolutionary branch, a not-so-glorious beginning of a new race, perhaps what our distant ancestors were to the Neanderthals. Naturally, the Sapiens are a notoriously violent race so any challenger will have a very hard time trying to knock them off the throne.

To survive and establish the foothold, the mutants must have a specific purpose (to explain why they weren’t exterminated before) and their own source of strength (to explain why they haven’t been enslaved yet). The best way is to tie all three (mutation, purpose, strength) together:

The mutation makes them uniquely suitable for the engine/reactor work, which no ‘normal’ human would be able to do, which is enough to ensure their survival. This same talent makes the mutants the best scavengers, able to explore areas that remain off-limit to most humans due to radiation, which means they have plenty of pre-Mutiny (i.e. Earth-made) tech.

Such tech isn’t exclusive to the mutants (they aren’t a twisted form of Fallout’s Brotherhood of Steel hoarding all the good stuff) but it makes them a well-equipped ‘faction’, capable of protecting themselves against random attacks.

Culture/Castes:

In the mutants’ earliest days labor was by necessity divided, the men tending to the engines while the women tended to the men as they inevitably sickened and died. Much was asked of these mothers and sisters, and from the beginning they adopted the Christian faith to augment their strength.

Many mutants credit their people's survival on this belief, that another world awaits them after death, a counter to the hellish reality of the reactor. Due to the inescapable radiation poisoning of engine work, only the females lived long enough to take on the role of elder, and to run those aspects of life beyond the perimeter of the engines.

Thus did necessity evolve into tradition, and tradition into law. The females sustain the priesthood and all the sacred duties of religion, while the engine work and protection of the enclave have fallen to the males. Those who aren’t happy with such an arrangement leave the enclave, becoming true outcasts, welcome in neither the Habitat nor the Covenant.

Party members:

You’ll be able to recruit either a priestess aka the Harbinger or an outcast aka the Wastelander (but not both at the same time as they won’t get along).

The Wastelander – a rather antisocial mutant who makes a living exploring the damaged areas of the ship and stripping them of anything valuable. Sort of the ‘mountain man’ of the ship. He had a falling out with the Covenant, so now he bears a special hatred for all religious folks, including the Church. Religion is the only topic that can get him all worked up, so don’t take him places where someone might ask if you have a moment to talk about our Lord and Savior. He will leave you if you join a faction, but if you’re a “burn it to the ground” kinda guy, the Wastelander is your man.

The Harbinger – a Covenant priestess tasked with spreading the true word of God in the Habitat and warning those who were unworthy to bear the Mark about the Judgement Day. A true believer, the Harbinger is convinced of the superiority of her kind for they alone will survive the Hellfire - the ultimate test that will separate the wheat from the chaff. She wouldn’t mind speeding things up a bit and will join you let you join her if you prove your worthiness (just because you're a member of a lesser race doesn't mean you're useless). She comes with unrestricted access to the Engine Room, so she's a good friend to have.
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