Helen's honeymoon with Bruce in Europe. He cheated on her with various men they met and called her a "stupid bitch" for not being able to read a map and trying to leave the car. Alison compares her to the heroine from The Portrait of a Lady.
Alison's horror on learning that one of her dad's lovers was Roy the babysitter, someone she idolized. It's a small wonder that she hangs up the phone after hearing that, since it's Et Tu, Brute? both towards her father for cheating on her mother, usurping her Coming-Out Story, and corrupting a trusted friend.
Alison's argument with her father as a teenager when he pushes her to feminize her appearance before church; what makes the scene stand out aside from all the other scenes depicted in the book is that Alison actually breaks down in tears after her father and sensitively asks her if she wants to look beautiful. the fact that her father won't accept her as she is is just utterly painful and true to life for many people with painful relationships with their parents.
Also, Alison wondering what might have happened if her father had come out of the closet and succumbed to AIDS during the 1980s epidemic, thus making his death more painful and protracted. These captions are juxtaposed with Alison putting up posters about the epidemic and pondering.
Alison not wanting to believe that her father's suicide happened independently of her actions, because she's unwilling to "let go of that last, tenuous bond."
Alison ending the story on the image of her father reaching out to catch her when she's jumping into the pool.
In general the latter half of the show is deeply depressing.
The opening number "It All Comes Back" Alison recalls her father finding linen and silver in someone's garage, and in the present comments on how ghastly it looks. She also wants to tell his story despite not remembering it well.
Maps has Alison considering the geographical span of her father's life, and realizing how limited it was. "I can draw a circle: You lived your life inside."
The scene before that also fits, when Allison is trying to get her father's approval of her art project, and she seems to nearly succeed, only for Bruce to flip out because she wanted to do the project differently than he did.
The last visit Alison had before Bruce died. She brought along Joan, whom Bruce treated as one of his kids by giving her silverware to polish. He was even going to take Alison to a gay bar and told her about his first sexual escapades. It's the only time in the musical that he never tried to change his daughter, which created a Hope Spot that they could live with his mistakes and hurting Helen. Alison had no idea her father was suicidal, and it was just as he was accepting her for who she was.
Days and Days is Helen confessing all the sacrifices she had to make to maintain the family's life, including her own happiness, and forbidding Alison from following in her footsteps.
The very next song, Telephone Wire, might be the saddest and most relatable in the bunch. Alison recalls a drive with her father, and realizes it was her last conversation with him. She urges her younger self to talk to him with growing despair, to say something to comfort him, but she cannot change the past. "That was our last night."
"There must be some other chances, there's a moment I'm forgetting, where you tell me you see me! Say something! Talk to me! Say something, anything!" Just the way Alison's voice breaks as she sings those lines, directly addressing Bruce. It's also not Middle!Alison singing it; it's Regular!Alison who takes her past self's place.
Edges of the World depicts Bruce's last thoughts before his suicide. The musical's (and Alison's) interpretation is that he sees Alison come out, and feels he's missed his chance at truly living. With its strings, hoarse screaming, and subject matter, the song is almost frightening.
In Flying Away and the preceding monologue This Is What I Have Of You, Alison recalls all the memories she has of Bruce, and the moments she shared with him, concluding that for all his deep flaws, they would always have that perfect moment where they played airplane.
The final line of the musical.
"Caption: Every so often, there was a rare moment of perfect balance, when I soared above him."
On a meta-level, Alison remarked that her mother, who was living while this was on pre-production, never lived to find what an rave the musical became or even see (or refuse to see) the musical. Alison also hopes that the show was in some ways, a form of healing for the spirits of her two deceased parents.
The Tears of Joy version of a tearjerker in the form of "Ring of Keys." Small Alison realizing that maybe she's not completely abnormal for wanting to dress the way she does is just so heartwarming and beautiful to see. This hits home when adult Alison is watching her younger self sing with hope and joy.
I know you. I know you.
This also applies with Changing my Major. Allison was in a position in her life where she's scared, lost and confused about who she really is. And after her first sexual encounter with her roommate, how happy she is when she suddenly figures herself out and finally stops trying to bottle up her sexual feelings towards women and a lot of LGBT+ Youth have had those moments. Changing my Major is a song about self discovery and teaches young LGBT audience members what no matter what you identify as, it'll turn out okay. You'll be okay.
Just the completely overjoyed way Alison delivers the line, "I thought all my life I'd be all alone..."
In context, Raincoat of Love is actually quite sad; the entire number is a fantasy sequence that Alison imagines to get away from her parents' arguing. She dreams about her family having fun and being happy, living a life where "everything's alright", when in reality, it isn't. The real kicker is that Middle!Alison and Joan join in on the dance, further emphasizing that this is a fantasy sequence.
"What did it feel like to step in front of a truck, Dad? What did it feel like to see it coming right at you, and not move? And just — let it hit you? Why?! Was it because of me...? I'm afraid it wasn't. That's the crazy thing, Dad, I'm afraid it wasn't!"
Allison was only 20 when she found out her father killed himself. And we never got to see her brothers John and Christian's reactions to Bruce's death.
Regular!Allison's near panicked tone in voice in the song "Telephone Wire" really says something about how much she wanted to change fate and give her father comfort, but ultimately couldn't as it's only a memory and she can't do a thing.
"Helen's Etude" fits too, with Bruce seducing a former student as Helen plays piano in the next room. Her Stepford Smiler side really shows through. "Maybe not right now. Maybe not right now."