A society that they intruded upon. If it werent for them coming to the ark then the war wouldnt have happened, im sure there were some other survivors out there. I find it strange that the resistance had to run away from the mainland to the ark for help, but they want to go back to it. Why didnt they just stay on the mainland in the first place. If its all flooded, then why do they want to go back to it.
It's a legitimate thing to want. The Ark and the mainland have access to different resources: the Ark has a fully functioning infrastructure and self-contained economy, able to manufacture complex modern machinery. It is full of scientists who have exactly the knowledge required to cope with the collapsing ecosystem and suddenly changing environment, and engineers who specialise in tools for sustainable local economies, like solar panels and wind turbines for power, and renewable construction materials. What the mainland (or what's left of it, anyway) has is
natural resources, like land for crops, metal for tools, and lots more fresh water. Ideally, if contact were established, trade could begin and the technology used on the Ark could be used to rebuild civilisation, while the resources coming back from the mainland could alleviate many of the Ark's problems.
Of course, humans aren't always that cooperative with each other, and what it's crucial to remember is that the mainland also has lots of guns and ammunition. Ever heard of NORAD? It's the North American command center for U.S. and Canadian military forces, and it's built into the Rocky Mountains, over a mile above present-day sea level. So that'll still be there, which means what remains of U.S. leadership definitely has the resources to take over a tiny island like the Ark if they think it's useful. The only problem is that the floods destroyed all the harbors. So making an effort to contact the mainland, sending out ships and such, could be catastrophic, because anything the Ark's inhabitants do that allows trade or exodus will also allow invasion.
There's not an easy answer to this question, hence the appeal of the game: it pits altruism against altruism, one side fighting for the survival of the species and the sanctity of its accumulated knowledge and expertise, and the other fighting for its dignity and ethical integrity.