90s teen novel about an alien invasion in a small farm town. Showdown in the school at the end of the novel

This sounds a bit like it might have been a novelization of the movie "The Faculty" from 1998. The following Wiki site has a promotional movie poster cover that matches what you describe as the book cover. As you note, only the kids are aware that something is going wrong and start getting killed off. Too, the showdown does occur at the school with the kids being able to defeat the alien leader. Finally, the aliens in the film are found to have a weakness due to:

However, I don't specifically remember a scene with a tractor running over a kid.

Wiki Cover

Does this sound familiar?

https://en.wikipedia.org/wiki/The_Invasion_%28Animorphs%29

I've been looking for the same book for years. I read it as a kid on a trip to Disney World. This is the closest book I've found that vaguely feels like the same as one I read, but I don't know cause I don't really remember it that well. I always thought it was more of an obscure book, kinda let down if it was just another animorphs.

I was looking for the same book and found this thread via Google. It's the Visitors series by Rodman Philbrick, starting with Strange Invaders.

Twelve-year-old twins Nick and Jessie are woken up in the middle of the night by a blazing white light followed by a loud explosion. As they rush to the window, rain suddenly begins pouring down, and the water starts to glow. It is the strangest thunderstorm they’ve ever seen, and it stops as quickly as it started.

Nick has a feeling it may not have been a storm at all, but visitors from another planet. When he and Jessie decide to investigate a strange sound downstairs, they find their mom and dad digging a hole in the basement. At least, they think it’s their mom and dad. But since when does their mom let them eat all the junk food they want, and why isn’t their dad going to work?

Nick and Jessie know something is wrong, and if their hunch is right, their parents’ bodies have been taken over by aliens. It’s up to Nick, Jessie, and their best friend, Frasier, to solve the mystery and protect their town from an extraterrestrial threat.

The Dark Side of Nowhere by Neal Shusterman?

• Small town kids who notice parents are acting weird
• One of the kids dies early on and rumors spread as to how
• Kids receive monthly shots and are told it is "medicine"
• One kid's parents don't cry at their funeral
• One of the parents reveals to the kids they are aliens
• Alien plan was to scout planet before returning home to plan an invasion
• Protagonist does not want to leave human life behind, so he fights against the adults' plans

There is a spaceship involved towards the end but I do not recall if any final confrontation takes place in a school. Also, no memory of there being a weakness apart from needing the "medicine" or they will revert back to their alien form. Read this in middle school and it was sentimental to me as well.