I mean... I don't doubt that something very horrible is going to happen, but I also feel like people really overrate Hope's warning. Hope did next to nothing for nearly three chapters. I feel like if Hope really wanted Sensei to take whatever he's meant to take he would have taken drastic measures much sooner. My personal guess is that "something bad" will be slightly darker than what we've seen so far to gradually shift the tone of the story towards darker stuff for the future chapters.
Also, since there are 35 heroine routes at the end of the story, I think we can probably expect all the girls to be alive and well by the end of the story.
Biding his time, perhaps, just waiting for the perfect moment to strike. That time may be drawing near. As for why he didn't act sooner, this could have been a test of Sensei's resolve and, assuming he does not heed HOPE, he fails. Then there's the possibility HOPE wanted Sensei to do it under his own power instead of the influence of the gods, only using the threat of consequences as pressure instead of forcing Sensei to act like what happened previously with the Yumi kiss according to Sensei's own words.
As far as everyone being alive at the end of the purity routes, remember that all those purity routes are said to be individual focused, so they won't be reliant on all the girls making it out of this alive. The only one that has to survive, and that's only up to the very end and then she can die as part of the ending of the route without issue, is the one the route is for.
It's already been demonstrated that death in this game is a temporary condition.
For now, we also don't know exactly how far that 'protection' goes. There may be something down the line that results in a final death. Anything from something the gods themselves can't even prevent to the gods wanting them to die for whatever reason. Perhaps Sensei continues to refuse them after the consequences already laid out in previous events once those are delivered.
Like I said, we're likely about to find out. The warnings could be overrated. HOPE has also apparently just been generous and waiting until that warning:
In other words, HOPE seems to have lost it's patience and might actually stop being so nice now. Or as it seems to put it:
It will take everything.
Personally, I'm more worried about the girls being reset than them dying. I don't really think I'd enjoy the endings with empty dolls that look like the girls I've grown to know.
Everything of yours, that does NOT sound like threatening a full reset, it sounds like it goes far beyond. That sounds like he's thinking of going after the girls, particularly ones with a history of intimacy, ones Sensei may have at least a little feelings for at this point.
I think Toys was a demonstration of what the consequence might look like, since it showed us that Angels could hijack people and turn them into puppets.
That, plus the Halloween scene with Molly two years ago, point to a very uncomfortable scene brewing. They're gonna bodyjack Akira into doint what they were trying to get him to do on his own free will.
Very possible, I could see a full blown rape in the future with Molly or another untouched girl on the receiving end, Molly specifically because
she was already targeted once and it failed. That's already setting up a potentially very uncomfortable scene.
I'm thinking it's just raping a teen. Maybe a virgin in particular. It seems like something/HOPE has been trying to make him rape the girls for awhile. Yumi in Chapter 1, Molly in Chapter 2, and Sana in Chapter 3, for example. HOPE may have just got tired of waiting for Sensei to rape one of his students, so is more or less saying rape or I'll rape for you.
Long Maya actually seemed interested in how Sensei "managed to avoid violently raping anyone" back during 'The Room with Clocks':
So, yeah, I'm thinking that's what the "take" thing is about.
Could be wrong though.
That's been my running theory since it came up, something he isn't supposed to have, their virginity is a prime target, particularly the virginity of a girl that hasn't consented yet and hasn't shown willingness to do so.