Spoilers to follow, so be warned.
A new plot summary showed up on IMDB, which builds upon what we already know about the film and adds some significant details. Now, anyone with an IMDB pro account can post summary's like this, but it doesn't seem to be a coincidence since the Logan trailer has already been classified and is expected to drop sometime tomorrow. You can view the plot summary below.
The biggest reveal here is Nathaniel Essex's role, though the fact that the X-Men no longer exist is also crucial. It was known that Essex, also known as Mr. Sinister, was going to be involved, but no one knew in what capacity. Here it seems he is in control of the very thing destroying the earth and possibly had a hand in destroying the X-Men.
If that is the case, it will differ from how they died in the Old Man Logan series. In the comic, Mysterio altered with Logan's perception, and Logan commenced to defending the school from enemies like Omega Red, Sabretooth, and the rest of the X-Men's rogues gallery. Unfortunately, he then realizes he's been fighting his teammates the entire time and has managed to kill them all.
The tone of the film will indeed be dark, but this scene, in particular, is brutal, so it remains to be seen if they will go that far.
Xavier is also revealed to have Alzheimer's, which explains why his powers are fading, and X-23 is confirmed. The studio will likely release the official synopsis in tandem with the first trailer, so we'll just have to wait and see if these details pan out.