To borrow a line from one of F. Paul Wilson's sf stories, "Wheels within wheels...". There're clearly several different plot threads going here, including the corrupted Ravenclaw sisterhood (one hopes they can be cleansed and redeemed). The bit with the grenade was a nice touch.
With that ending, I'll be interested in seeing who died besides Remus and why it has Harry so beat up. On the other hand, while this chapter is most definitely a "downer", I suspect that it contains the seeds to inspire future actions on Harry's part. Between the intense love, physical, spiritual,a nd psychological, growing 'tween Harry & Hermione and the fact that Harry's not the kind to gladly suffer the death of friends, I can see that Tom may have won a battle but ultimately lost the war. For that matter, while it's not been stated, I suspect the first section cearly shows Hermione finding both the reason and the tools for finding a way to survive and, in her own way, she's every bit as stubborn as Harry is.
It was interesting to see Tom re-embodied early and I wonder who'll detect the substitution when "Moody". Personally, I don't think he realizes just how good and experienced the Brotherhood is and how much interest they take in Harry; that's bound to come around and bite him one of these days.