Kei goes into the arc expecting to overturn canon. She fails. Her personal Butterfly of Doom kicks in, and Kakashi is grabbed instead of Obito and despite Team Minato's best efforts. He's put through a field interrogation that results in the loss of his eye. While Kei and Obito do manage to kill the two Iwa jonin, because they underestimate the two chunin, Obito is still caught in a rockfall while saving the lives of his teammates. He has the longest death scene of any character in the story.
Obito: "Kei...go. Please...don't let him die. He needs to...to keep his promise." Kei: "N-No, I can't..." Obito: "...I'm not going...anywhere, Kei..." Kei: "...I'm so sorry. I'm sorry I couldn't... I should have done something! You shouldn't be stuck here..." Obito: "Heh... That's just l-like you, Kei... G-Go. Move forward..." Kei: "I...okay. Okay. You win." ... Kei: "I know... (Im sorry.) Sleep well, Obito... I...we'll see each other again soon." Obito: You...know it...
But this is impact is eventually mitigated by Obito's reappearance one timeskip later.
The Commencement Arc:
The body count for the arc includes Kei and Hayate's mother Miyako.
In the aftermath, Kei and Hayate spend the next few chapters (and a timeskip) grieving in various degrees of visibility.
The Bloodlines Arc:
Obito finally has a long-overdue breakdown due to the group finding out that Madara died not long after the events of the Commencement Arc. The latter character's death isn't viewed as a tragedy by anyone else, but they stay to comfort Obito as the Stockholm Syndrome finally rears its ugly head.
During the battle for Sorayama, Kei's team—consisting of Gai, Genma, and Ebisu—ends up getting split to help the civilians evacuate while dealing with threats. While Gai and Ebisu are fine, Genma is caught unawares by Orochimaru and gets beaten half to death. Not long after he's saved from immediate danger, Raido's team runs across the field hospital. His reaction isn't optimistic.
I lean down over Genmas face and press my lips to his forehead. If I concentrate, I can just barely feel his breath, weak though it is, brush against my right ear. Hes alive, still. But thats all. I just wish my thoughts could get through to him like this, but they cant. Im sorry, Genma. Even if you wake up I...dont see how this will work out. Goodbye.
The lives of the jinchuriki are generally unhappy affairs, brought to the forefront by the number of them in the cast who can finally commiserate over their experiences.
Though Yugito is very loyal to her village, she's as affected (read: guilt-ridden) by the offhand mention of being used as a human weapon as Kei is.
Side stories reveal that Utakata's childhood was very isolated, and he values his pirate friends after their deaths because they accepted him and Saiken instantly.
Han outright says that he'd much rather continue babysitting a tiny civilian milkmaid on an island in the middle of nowhere than go back to his village.
Gaara is clearly much happier with the Straw Hat Pirates than he ever was in Sunagakure, and even admits that he and his siblings aren't close.
Kei's childhood was sacrificed for the sake of keeping Naruto and Kushina safe, even if she made the choice willingly.
Ace's POV chapter takes place in Impel Down as he's awaiting execution. While chained to the wall with sea prism stone to keep him from escaping, he has a lot of time to think about how much he's failed his loved ones by being captured. He mentally apologizes to the Whitebeard Pirates, his brother, and even his new jinchuriki friends for leading them into trouble. The only thing that lifts his mood is when Jinbei is crammed into his cell, and Ace ends up telling the most reasonable of the Seven Warlords about Luffy.
More than once, Kei makes a Call-Forward to what is referred to as the "hell year" by the readers. The issue comes up each time Kei makes a remark, mental or otherwise, that downplays her life's value or her past traumas.
Hitoshi's self-esteem is clearly through the floorboards, thanks to constant rejection of his Quirk and therefore him as "villainous." He tends to lash out verbally at people nearby, and was well on his way to not having many friends before Kei sorts him out, even if she's not necessarily the most forthcoming person.
Kei and Hitoshi have a falling-out late in the Sports Festival, and Hitoshi briefly has a moment of pure emotional confusion when, instead of cutting ties forever, Kei leaves a token of their friendship with him while he's unconcious. Until Homura shouts him into order, he doesn't even know how to begin approaching patching up any hurt. He clearly hasn't had many friends before.
During the raid on the training camp, the UA students' terror amid the attackers really shows that they are just kids learning to be heroes. They panic, cry, or otherwise freak out while in life-threatening peril, even while fighting back. For Kakashi's part, this means he defends the students to the point of risking injury that lays him out flat, but Kei instead wishes that she had some way to comfort them—but as Turtle, she can't.
Kei and Hitoshi have a difficult conversation while visiting a cat cafe, because Kei is not going to be in Tokyo forever. They've grown close enough that the thought of Kei leaving permanently hits Hitoshi hard. He's clearly not dealing well with it a chapter later, either.