I will preface this by saying I enjoyed this movie. If you have some interest in philosophy, sci-fi, religion, and global politics you might get some enjoyment out of the viewing. If you're looking for a good plot or characters, stay away. This movie is a prime example of trying to do too much but not committing. Gakuen no Himitsu had a lot going for it, but the great art direction in the second half of the movie (Vega was beautiful) was marred by a plot with too much stuffed in it and characters with no personality. This is particularly evident in the scene where the main castis on their way back to Earth. They just travelled >1000 light years, went to the spirit world, saw alien species on inhabited planets, and revealed to themselves their past lives. Like they're in class reading their essays out loud, each of the friends feels the need to chime in what they learned. The guy who has shown no interest in engineering or building things wants to build a UFO (they butcher this term throughout the whole movie, by the way), no interest in moves wants to be a filmmaker (probably the director/writer's projection), the anime otaku wants to be a teacher (this actually makes sense), one realizes it's okay to be introverted and be yourself, and the last one wants to figure out a path forward for Earth.

Lets's talk about that title. Which school are they talking about? And which mystery, because there are a bunch of small ones that don't seem worth naming the movie after. It seems like they were trying to go for a sci-fi thriller mystery with some action thrown in, but there wasn't anything mysterious about this at all. The audience pretty much knows what's going on as it happens.

As if exposition is the only story-telling device, the movie tries to hammer in a new point every 5 minutes. If the director/writer honed in on a central theme, the movie could have been much stronger.

It was slow at the beginning, they do a half-ass job character building, the story picks up in the middle, but then it all starts falling apart when the aliens start to fight.

The main cast had potential, but only the main male protagonist really did anything at the end. And even that was mostly to get the shounen tropes checked off.

Despite it's shortcomings, I enjoyed it as I watched. There were many times where I felt like I was being talked to (in a bad way); bringing the sledgehammer of "Let's make the world a better place" and "Be yourself" down on the viewer (listener?) over and over and over again. But there was an odd beauty to its ambition.