I've already considered this extensively. Note link below.
However, it would be nice to make each plague a mission that the player could carry out, or at least assist in.
Tainting, (or rather, fixing) the Academy water supply. Most likely, they have a way to collect and melt snow then clean the melted snow to get fresh drinking water. It's what I would do if I had to provide fresh water to a large facility in a place where it snowed constantly. It's a similar concept to a rain barrel just with a few more steps. The player would have to cut the fog infuser out of the process similar to how they do in Evergreen Meadows.
The Snowmoors have a frog equivalent in the Snowmoorian Scorpions. I know we see them as cute and fluffy, but Victoria and the Baron might not take so kindly to the little creatures. If there could be a way to bring scorpions into the Academy, or even the Grease Pits, that might cause some mayhem. The player could open air vents and set up artificial scorpion nests, in other words, make the Academy a good habitat for scorpions with their claws and stingers.
Irving created little, clockwork, beetles that scurry around like the real thing. He gives them to the urchins as toys, but an entire horde of them would be less well received by adults. The player could sneak around the Academy releasing jars of beetles in strategic areas.
Collecting the moths that fly around various lampposts in Aethasia and releasing them into the Academy would be a fun mission. Lucas could give us special bug bottles for that purpose.
Widespread destruction of automatons lead by none other than Emily herself.
The player could introduce snake venom to the Academy food supply causing all the residents to throw up, repeatedly. After the Baron seems to relent, as he shall repeatedly, we lay off the venom and the Academy brings in new supplies.
My favorite one of all! Full scale assault! Ground-to-ground bombardment with heavy artillery positioned strategically throughout the Snowmoors, perhaps on the deck of the Blessing itself. Bring out the big guns and load them up. Let's bring that monument to evil to it's knees!
We bring Snowmoorian crocodiles into the Academy and the hungry creatures eat EVERYTHING. The Academy completely runs out of food.
That is one idea, but there is another. Jefferson could build a weather machine that unleashes a blizzard unlike anything the world has seen before or since. The snow and wind are so terrible that the player must use the dreamweaver to see anything while outside. Inside, the Academy has lost fog generator due to the storm so light and heat are not available. The player may even sabotage the main boiler and cause the darkness. The cold and dark almost break the proud Baron, but not quite.
Not just any boss, THE boss, a project on which the Baron was banking his hopes. The whole reason he seemed so stubborn was that he was betting everything on this ultimate automaton to destroy the Resistance once and for all. He's played our game for long enough and the automaton is complete. He is ready to unleash it upon us and win, what in his mind, was a terrific gamble. However, the player gets to it first. With the Scarlet Man on one side and Emily on the other, we take down the most powerful automaton we have ever faced. The Baron lets out a gasp of disbelief as he finds his last line of defense gone. With nothing else to hope for, he finally surrenders. The Aethasia's blessing is free from its icy shackles.
However, the story is not over. Just as the Resistance flagship is ready to take off into the sky, the Empire arrives. It seems that Baron Fairrow is a sore loser and told Lucky that we had been messing with him. Lucky, also a sore loser, sends his new flagship to take back the Blessing. What follows is two airborne warships firing at each other with the player avoiding shots and returning fire with the Blessing's arsenal. All this ruckus causes a thick cloud of smoke to come between the two ships and allows the Blessing to escape while the Empire's ship crashes down into the very ice that once held the Blessing prisoner.
This could lead into a couple of side missions that involve making repairs to the Blessing, clearing our captured prize of automatons, and hooking up the Snowmoorian Great Engine to its new power booster. We could call it, the Great Escape or something like that.
Who else is under the impression that I have too many brain cells to spare?