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How about some more aggressive scavenger animals. Jackals would pass through the area and be attracted to things like exposed corpses. This would make leaving corpses unburied outside of your base (say in a garbage dump as some players are know to do), a bit more of a problem. The jackals would of course eat the dead bodies but then would likely stay in the area digging out a den for themselves, and if it gets hungry it would likely go after other animals first, but then again... well it already has a taste for human meat so it may attack one of your colonists who is out on their own without warning, or it might go off digging up unattended graves, causing problems for your colonists morale. Another problem would be rodents of all kinds. Rats burrowing into your freezer, mice building a nest in your walls, all of them stealing your food, and spreading disease. It would be interesting too if rabbits would tunnel around the map or dig out a hole under your wall so they could steal some crops and make a run for it. Some other ideas would be bears and large cats.

What if after so many defeats at the hands of your colony hostile factions would become intimidated, or discouraged by their losses. After your colonies intimidation factor gets high enough it enemy colonies would hesitate for awhile before attempting another attack. Your intimidation factor would decay over time but might buy your colony enough time to recover between attacks. There might be a way to extend or to artificially inflate your intimidation factor, say by hanging corpses near the edge of the map or by keeping prisoners hostage. To increase your intimidation factor you could hold on to prisoners, beat them for a while, and then release them so they can tell stories of how horrible you are (hopefully) scaring others into not coming after you. Or you could go onto the comms consul and spread rumors about how formidable your defences are, or what you do with your dead foes. Of course you would risk damaging relations with the friendly colonies, and your colonists will not be all that happy about hanging corpses and beating defenceless prisoners.

How about a moodlet called something like adrenaline rush, that would apply in moments when your colonists are in or witness someone in imminent danger (proximity to an explosion, gunfire, being sent to rescue a colonist, being attacked obviously). It would give a somewhat significant boost to their mood, say around 30-45 points, either until shortly after the threat is dealt with, or after significant amount of time (around a two to three days). During that time the colonist would not be able to sleep or eat, would move faster, be able to carry heavier loads, shoot more quickly, and hit harder. After the moodlet has worn off the colonist would get another moodlet, an adrenalin crash, that would give a negative mood effect relative to the length of the adrenaline rush, which would wear off after they have done something to boost their mood (eat, sleep, have a conversation, etc).

What if you could set a character to improve relations with another colony, a third option when you open communications with another colony. It wouldn't have to improve relations very quickly but over time a character would be able to improve relations with other colonies without paying silver, possibly reducing the price, or changing what they want in exchange for more cooperation. Of course having high social skills would speed up the process, but the idea is that it could take years to max out a relationship. Raising relations as little as one or two points a day. Characters with a high social would more rapidly raise relations and might get access to special events, for instance being warned of an attack coming your way, or maybe a trade of goods (medicine for potatoes, guns for metals, only strangers trade in silver afterall). Another idea is that there could be a risk of failure with low skilled characters or characters with certain traits, where rather than improving relations they would be damaged.

What if exposure to certain mood effects, both positive and negative, resulted in characters building up a sort of moral immunity to them? Say your colony is in region that is persistently cool. The first year or so they may complain about how cold it is but over time they come to accept the cold as a part of their day to day life, possibly even exhibiting a higher tolerance for colder climates. Or say your colony is under constant attack, your colonists may become less effected by killing people, and being exposed to the unburied dead. There would obviously be consequences for these adaptations, for instance, a colony that is constantly suffering from food shortages may become less hungry and therefore save on food, but they would also be more prone to sickness and would become exhausted more quickly, a colony pushed to cannibalism too often may develop a taste for their fellow human flesh (or even become dependent on it), the people of a colony that has seen extraordinary amounts of death may lose all value in human life and pull guns on one another for the slightest disagreement. sort of like how dwarves in DwarfFortress can become intolerant to sunlight.