After El Terre is gravely wounded in a fight with Swilium, Alice is seen at his side in the Nurse's Office, hoping that he'll pull through. And this is before they confess their feelings for each other.
Day Two cranks up the tear-jerking factor. First and foremost: Christine's death is revealed to be set in stone, as part of a complex, apocalyptic prophecy. One day, after the signs have occurred, she will simply die, and the winds will cease. That this is heavily implied to be a curse from Nether does not help matters.
We see a brief glimpse of one of Aqua's traumatic memories of Trigan. The fact that Pontoon reveals that she was used in several of his experiments does not help matters.
The scene where Trigan murders Atiago (he gets better), Haven, and the Experiments in cold blood just outside the Main Gates.
A short while after Trigan is exposed for the murders, James and Lily share a few drinks in the teacher's lounge. He opens up to her, confessing he's afraid for the future of the Academy. The school is his life's work, and if it closes down, whether due to a villain-related incident or not, he'll have nowhere else to turn, as his family has essentially disowned him.
After unintentionally injuring Dahlia with his super-heated skin (just as they are about to make love, no less), Fury is traumatized by what he has done. In sheer frustration and anger, he ends up briefly giving in to his Superpowered Evil Side and wrecking some property in the lobby before being subdued by Magi and Simon. Later, after being subdued, he heads to the former's office to talk about what's troubling him, and he is visibly torn up over everything.
After a botched prank where she pretended to be his conscience, Willow and Adrian have a telepathic heart-to-heart, talking about how they came to be. She recounts her horrific past as a test subject for Normco, and how it colored her perception of the world, while he talks about how he's become disillusioned with the world for all the evil he sees in it. When he's talking about his past relationship with Valerie, he oscillates between bitter and wistful.
Talan tells Lightning about a traumatizing incident—when he and Helena were still together, she dared him to put on a dress for her. She ended up taking a photo and circulating it, humiliating Talan nearly to the point of suicide. He breaks down crying in front of Lightning as he recounts the incident, showing a rare moment of weakness. Feeling awful for having just playfully dared him to put on a cute dress for her, she takes it back and reaches out to hold him, calming him down.
After Jane's initial belligerent encounter with the two, James explains his fear of her to Lily. Nine years prior, Jane had gotten James drunk at a bar—he was still just lucid enough to refuse her—then dragged him to her home and raped him, all for the purpose of obtaining a child to perform experiments on. To top it all off, she lied to James, saying that Jackson was stillborn. Lily is stunned to hear the truth, immediately apologizing for bringing it up.
Atiago's messy divorce with Rose, complete with the revelation that she was cheating on him. This sets up an even bigger Tear Jerker later on...
During Atiago's battle with him in the forest, Chrys freezes time to explain to Lily why he has come for Atiago's life. He explains that Atiago was resurrected with a lifelink with Rose—essentially a spiritual/romantic bond between two people, manifested as a sort of Red String of Fate; in Atiago's case, it was keeping him alive. And now that she has broken his heart, the lifelink is severed and he is now Living on Borrowed Time; unless someone takes over the lifelink for him, he will die. Lily is conflicted, being forced to choose between letting Atiago die or breaking James' heart (the latter of which would lead to James breaking down, or worse, and the school would suffer for it). In the end, Chrys departs, giving the group their ultimatum to find someone to willingly share the lifelink with Atiago.
In the same scene, Chrys actually grabs hold of the lifelink between James and Lily and squeezes it, causing physical pain to both. He expresses delight in torturing them, threatening to break the link.
Lily, having suffered both immense physical and emotional pain from their encounter with Chrys, embraces Atiago and cries into his shoulder—the first time she ever shows vulnerability around anyone in the school.
Every.Heroic.Death. Christine, El Terre, Swilium, Alice, Krion, Dahlia, Foremen, Alderon (sacrificing himself to save Foremen), and Kivuli all sacrifice themselves for the group one by one. Eventually Nether's curse is undone, but nobody knew at the time that that was possible; their imminent deaths were a very clear and present danger for them.
Valerie is visibly torn after Christine's death, almost unable to react to the carnage around her—and then starts unleashing all hell on Nether.
And after the battle, after all is said and done, she simply collapses into Simon's arms, crying softly.
After the battle, Alexei is seen mourning his fallen soldiers, picking up their dog tags.
The ending, combined with a Crowning Moment of Heartwarming. Christine is brought back to life, and Nether's curse is undone by his death, saving the others. Everyone gets into either a group hug or a tender, loving embrace. Looking over the whole scene hand-in-hand, James and Lily prepare to rebuild the school together.