Rough summary of Volume 2 (Chapters 5-8): After the demon (Alice Kyteler - going to call her Alice Sr. from now on) teleports them, Alice and Mari end up back in Mari's hometown. It's revealed that Mari's mother was a witch who fell in love with a human and went into hiding. Alice and Mari decide to go to Mari's old house and wait for Dolly to find them. They find her house burn down, and her parents dead. Dolly arrives and brings them back to the academy. Dolly's backstory is shown to the reader - she was in love with a human girl who was brutally killed and has pinned all her hopes on Mari's resurrection ability. She's not actually interested in revenge; she just pretends to be. Alice is removed from being Mari's tutor by Dolly, though, since Dolly knows that Alice is in love and that Alice is prioritizing the safety and health of Mari over the resurrection of all the dead witches (plus Dolly's love interest). Alice suspects that resurrecting that many people from such incomplete forms (all Dolly has of her lover is a strand of hair) will likely destroy Mari.
Rough summary of Volume 3 (Chapters 9-12): Alice Sr.'s backstory is revealed - she was in love with a human but both that human and other witches betrayed her. As a result, she seeks to destroy all humans and all witches. She made a pact with a demon so that she could become a demon and never die in order to live long enough to see her plans come to completion. Alice Sr. leaks the plans of the witches to the outside world (they had apparently instigated a series of events to start the equivalent of a World War), and as such, humanity rallies together to destroy all witches. Witches are massacred en masse, and the school is attacked.
Meanwhile, while Alice and Mari are separated, Mari learns that Alice is in love with her and then realizes that she loves Alice. Alice and Mari meet in the school's graveyard for the first time in a while and are interrupted out of their love confessions by Dolly, as the school comes under attack. Alice shows Mari how to find her mother's corpse (which Dolly was planning to use to lure Mari into doing a mass resurrection) out of all the other corpses in the graveyard. Alice promises that she'll hold off Dolly while Mari resurrects her mother and then they (the three of them) can escape together. Alice fights Dolly to keep Mari from harm and realizes how powerless she really is but pulls enough strength together to crack the stone ceiling, killing both herself and Dolly (but not before finishing her earlier love confession).
Mari, seeing Alice's death, fully controls her power for the first time. Alice Sr. teleports in and attempts to stop Mari before she can cast a spell because Alice Sr. realizes that Mari's power was never resurrection at all (which is how Alice Sr. was planning for the humans to be destroyed too) - Mari can actually control time. Mari looks at Alice Sr. and can see into her past. She suddenly understands that Alice Sr. is where this is entire sad state of affairs began - her childhood, specifically. Mari steps into Alice Sr.'s childhood and prevents Alice Sr.'s mother from destroying her heart. This change has ripple consequences, and all of reality begins to shift.
Alice Sr.'s backstory is shown again. This time, she's more committed to helping humans and isn't betrayed by the people she cares about. Dolly's backstory is shown again. Alice Sr. has helped to create a cure to the plague that Dolly gets blamed for, causing the villagers of her town to protect Dolly and her love interest from the witch hunts that the villagers now think are evil. Mari is shown at this point disappearing into nothing, having completely burned through all of her power.
Rough summary of Volume 3 Epilogue: In the new reality, Alice and Mari are shown meeting at a Japanese school in the present day (because witch and human schools aren't separate, presumably). Alice is a transfer student who has just arrived in the country and is staying with Mari's mother (she says that Alice is the daughter of a 'friend' who is staying with them for the school year - implying that unlike the old reality, Mari's mother and Alice's family are friends rather than enemies). Mari feels that they've met before somehow, and Alice makes Mari a magic herb pouch to help her sleep, mirroring their initial interaction in Chapter 2... presumably they live happily ever after.
Obviously that leaves out a -lot-, and all of this is very well drawn and very heart-wrenching/heart-warming (depending on the part). I'm really happy with how it turned out - better ending and general plot than 80-90% of Yuri manga. Definitely something I'll be reading again in the future.