Quirrel seems on the road to get the Philosopher's Stone. It's certainly possible that he will fail or Harry ( / time-turned Cedric Diggory) will manage to swipe it at the last minute. But with around 80k words left to go, there doesn't seem to be a whole lot of story left if Harry gets the stone in the next couple of chapters.

I draw your attention to a few quotes concerning the Philosopher's Stone:

His strongest road to life is the Philosopher’s Stone, which Flamel assures me that not even Voldemort could create on his own; by that road he would rise greater and more terrible than ever before. (Chapter 61)

“It’s not a secret.” Hermione flipped the page, showing Harry the diagrams. “The instructions are right on the next page. It’s just so difficult that only Nicholas Flamel’s done it.” (Chapter 87)

“I was looking to see if there was anything here I could figure out how to do. I thought, maybe the difficult part about making a Philosopher’s Stone was that the alchemical circle had to be super precise, and I could get it right by using a Muggle microscope—” “That’s brilliant, Hermione!” The boy rapidly drew his wand, said “Quietus,” and then continued after the small noises of the rowdier books had died down. “Even if the Philosopher’s Stone is just a myth, the same trick might work for other difficult alchemies—” “Well, it can’t work,” Hermione said. She’d flown across the library to look up the only book on alchemy that wasn’t in the Restricted Section. And then—she remembered the crushing letdown, all the sudden hope dissipating like mist. “Because all alchemical circles have to be drawn ‘to the fineness of a child’s hair’, it isn’t any finer for some alchemies than others. And wizards have Omnioculars, and I haven’t heard of any spells where you use Omnioculars to magnify things and do them exactly. I should’ve realized that!” (Chapter 87)

So we have multiple mentions of the possibility of creating a Philosopher's Stone. We also have Quirrel's promise not to kill anyone within Hogwarts for a week. And Flamel may still be out there, with the knowledge of how he created the Stone in the first place.

All this leads to the possibility that Quirrel gets ahold of the current Philosopher's Stone, and Harry learns enough in seeing the stone in person to be able to recreate it using a combination of magic and technology.

You can't transfigure anything that doesn't exist yet, so just having a Stone doesn't mean an instant singularity. You can't just will a superwizard or an AI into existence. This leaves plenty of space for a war between two sides, both of which have permanent transfiguration at their disposal.