Have a suggestion for one of the mid-late game alien races. It doesn't matter too much aesthetically which race but I think it might an interesting mechanic to the game to differentiate this race over the others...
One of the Alien races has a plague or airborne disease. You don't know about this until your first encounter with the race. Perhaps this could be managed one of two ways,
1. Any soldier within 2-3 tiles of this alien, either alive or dead has a high chance of contracting an illness. This would mean that soldiers storming the alien ship will almost certainly contract it - while others may not.
2. Any soldier taking part in this mission without vaccination contracts the illness.
Effects and Consequence
Effects of the illness are not immediate and only discovered upon return to base. Infected soldiers are automatically sent to the medical bay to recover for some period of time. There is a reasonable chance that without a vaccine each soldier will die within 1-2 weeks (or some other game-balanced time). However, your scientist immediately come up with a program that can be researched to stabilise infected soldiers, which removes their chance of dying. This should be possible using only the initial research lab space (to avoid the unlikely chance of people auto-losing these soldiers because they don't have enough research capability).
Future soldiers that take part in missions against these aliens and become infected only spend a few days (or some random amount of time) in the med-bay under quarantine and recovery. This means you are not under any danger, but you do have to consider that soldiers on missions against this race will likely be out for some time upon completion forcing you to rethink what balance of force you take on the mission.
After your first experience of this illness, you can complete a new research option for a vaccination. This will initially be a race against the clock as you may have one or more (potentially experienced) soldiers infected with a very high chance of dying. This might cause an interesting conundrum for players - do you switch all your scientists onto a vaccination or do you let your soldiers die and focus on researching the next super weapon.
Obviously the idea needs some work but I thought it might add a little interesting variety as-well as a lore friendly "oh sh*t" moment in the middle of the game once you realise half your top soldiers are about to die unless you immediately switch your research priorities.