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In mission 1 of Chapter 2, the population is getting sick from rotten fish, and I run out of food. How do you resolve this problem?
I'm not sure if you can get the "fresh fish" item from the cove to the north in mission 2. You might have to wait till mission 3.
Setup a trade route to sell rotten fish, and buy good fish. In the meantime keep following the quest line to research antibiotics, after this the issue should be resolved.
To get rid of the rotten fish, finish Chapter 2 Mission 1 then continue playing Mission 2 until Eve gives you a quest to build a Weapons/Munitions factory. Finish that quest, then do her next fish net quest, and you will restore your fish.
In my experience, you must do these 2 "side quests" otherwise you will not be able to go to Mission 3, even if you beat mission 2 (by buying the weapons instead of producing them yourself). I think this is a bug.
There will be a mission to accept when you first got the rotten fish event. You will need to click on Dr. Bartok's warehouse, and she will give you a mission to bring her 10 rotten fish.
Completing that mission will change your fish back to normal, but yeah, rotten ones do give more money.
During this mission, shortly after the rotten fish start turning up, you will settle the underwater island of Sondar. Once you've established this settlement, you will be able to produce functional food. You'll also gain the ability to set up a trade route shortly afterwards. Set up a trade route to take the functional food to your island. This will keep your population fed in the interim.
I settled the Eco island initially, and as a result I got a quest from the Tycoon faction by clicking on their island's warehouse. If you bring them the goods they request (some lumber and tools, if I recall) they'll give you the "Emergency Plan" which, when put in an item slot in your island's warehouse, will keep people from becoming unsatisfied due to food. (I don't know if the Eco faction has a similar mission if you don't settle with them at the beginning of the first mission or not, but I assume they do something similar)
The fisheries on your first island will continue to produce rotten fish, however. I found that idling them caused the rotten fish to stop accumulating in my warehouse, which kept the people from getting further sick. To idle the building, first click the building, then click the percentage in the middle of the lower right hand pop-up. This will stop the building from producing goods.
You could also sell them to the Tycoon warehouse, for 72 credits per unit. As the game starts you with something like 45,000, I didn't find this to be all that useful, but your priorities may differ :)
