As a novel reader, what is your reaction to the following proposed story outline (see details)

Realistic fiction in which an organization tries to take over a small town. The general mood of the story is sad.

Ending: The organization for the most part succeeds in taking over the town. The second biggest protagonist (in terms of importance) is killed by the organization. The biggest protagonist decides to leave town. Ultimately, though, the organization is toppled by opposition from a third-party unrelated to the protagonists. This is the last of a trilogy of stories. Assume no sequels. Prequels discuss the protagonists’ lives prior to the organization’s arrival.

My concerns (in order of priority):
1. Killing off the second biggest protagonist, a kind and lovable character introduced in the second story of the trilogy, might be a huge put off to the audience. On one hand, I seek realism, and bad things do happen to good people. On the other hand, (1) fiction is not real-life, and (2) in fact, some people read fiction to escape the troubles of real-life.

2. I risk running a Family Unfriendly Aesop. That is, the bad guys win for the most part. I don’t want a story with a message saying that evil is cool and that good folks die off. A story’s theme is crucial to that story’s overall appeal, and having a negative theme might also be a put off.

3. Given 1 and 2 above, I still need to keep realism in mind. Both the biggest and second biggest protagonists are shy college students. They could lead some demonstrations, I guess, but otherwise, they really could not do much to stop the organization from taking over. They simply lack the connections, money, and power to do so. (Yes, in real-life, young folks have affected lots of change. I am aware. However, they still need critical mass, something that is lacking here. The town is in a state of chaos and the organization’s takeover is actually seen as a good thing that would bring stability by many.)

Please help. Any suggestions you have would be greatly appreciated.