Casey's relationship with his father, particularly him stumbling into the shop after getting so badly beaten he can barely stand. Raph, who considers Casey his closest friend, immediately storms out in a blind rage seeking vengeance.
Mutagen Man, just everything about Mutagen Man.
The City Fall storyline is full of these, but the standout has to be Leonardo dreaming of his mother. "Hear me, child, and see... that this is no place for you."
Mikey leaving the family after Splinter kills Shredder.
Casey and April's Bitter breakup and the aftermath with both clearly hurting afterwords.
The finale of Chasing Phantoms... Harold severs ties with the Turtles after his ex-wife is hurt protecting him, devastating Donnie. The Turtles' faith in Splinter is shattered when he has Darius Dunn killed despite him being defeated, causing Raph and Donnie to join Mikey in turning their back on him. When Leo asks why, Splinter reveals he did it to push them away for their own safety, knowing that he'll have to do some terrible things to keep them safe and that they're safest, and happiest, away from the Foot Clan, counting on Leo to take care of them.
The next issue shows Michelangelo still grieving. And it doesn't help that Old Hobscoffs at his soulful eulogy and follows up with a harsh speech about how they're at war with Bishop and all others who would abuse mutants. Later, it's shown that Mikey's still sore about that, and sick of all the moral gray areas that they've found themselves in lately.
Also in that vision, take a look at each of the Turtles' faces. Raph looks grim, Donatello resigned, Leo rueful...and Michelangelo? His expression is a blank Thousand-Yard Stare, as if part of him still can't believe that this is happening. And yet, he's still lucid enough to sadly admit that Leo did what had to be done, and that there was nothing left of the Splinter that they called father.
Issue 92 ends on one heck of a sad note. It looks like transfer of the Foot from Splinter to Karai is going to go completely smoothly, despite their difference of opinion... right up until the subject of the orphans is raised. Karai insists that they be made into Child Soldiers, and Splinter adamantly refuses, stating that this is the one thing he will not budge on. Unfortunately, neither will Karai and what could have been a completely peaceful transfer turns into a declaration of war.
Issue 100, where Splinter sacrifices himself to stop Kitsune's father from being fully revived and wreaking havoc, by having his soul take Oroku Saki's soul's place in the afterlife, as a repentant Saki is the one person who can talk down Kitsune from her goals. While Splinter is happily reunited with his wife in the afterlife, his sons and their friends and allies have just lost someone very special to them all.
Issue 101. All of it.
It begins as we see Splinter's funeral and what has happened six months after his sacrifice. Raph defected from the team and is now a vigilante protector in Mutant Town with Pepperoni at his side, but has cut off all ties to family and friends, brushing them all off even when they try reaching out to him; Don is keeping it together the most, while Leo and Mike have sunk into a deep depression, respectively taking care of a greenhouse garden and a new pet cat named Klunk but doing nothing else except be lost in their own world. With the turtles as they are, Jennika feels out of place and currently goes back and forth between April's farm and Mutant Town, feeling like she doesn't belong anywhere without the Foot Clan and scared she may slip back into who she was prior to everybody's good influence on her, and making matters worse, Casey and her have officially broken up.
April herself is exhausted and drained from her job as Stockman's assistant and she barely interacts with her friends anymore, her duties consuming all her time and she just looks unhappy in general. Her apartment is an absolute mess that she's either too tired or too unmotivated to tidy up, perhaps both.
Mutant Town in general is this. Hob's mutagenic bomb affected a lot more people than expected, so Stockman erected a tall wall around an area of the city where all mutants now live without proper living conditions, while Stockman boosts his political standings by saying he's doing all he can to find a cure for those inside. Any mutant caught outside the wall gets tossed back in and any human inside the wall is arrested and tested to make sure they're free of mutagens. Alopex is inside, managing well enough by running a shelter in Mutant Town to feed and give support to people who have been unable to cope with their mutation, but times are tough and food is running low. The place is full of thugs who try taking advantage of those who can't defend themselves, even with Raph and now Jenny trying their best to keep the peace. Though not seen yet, Hob and the Mutanimals seem to have devolved into tyrannical thugs who only make things worse. And worst of all, there are mutated children all by themselves in the town, some either forcibly separated from their un-mutated families, and most heart-wrenching of all, some were abandoned by their parents after their mutations.
Issue 102, apart from further demonstrating how badly the core Turtles are still hurting from the loss of Splinter, reveals that they're not the only ones having trouble adjusting to the new status quo:
The Mutanimals have gotten split down the middle by Hob's new approach - Man Ray and Herman are blindly following Hob, Mutagen Man and Mondo Gecko have gotten fed up and skipped town, and Lindsey Baker was evacuated due to being a human. No word on Pete, but it's not hard to imagine the poor guy's torn up by what's happened to his family. As for Sally Pride, she's not at all happy with Hob's approach, but doesn't see a way out and is stuck trying to blunt the brutality being exercised by their new soldiers.
April's still trying to dial up the Turtles, who still aren't picking up the phone due to being lost in their grief.
Speaking of the Turtles, they barely speak to one another, despite obviously wanting to. When Donatello finally works up the nerve to ask how they fix this, Leonardo sadly remarks that there might be no fixing what's happened. This ultimately spurs Donatello to head back to N.Y. on his own, leaving Michelangelo and Leonardo alone.
This is especially hard on Michelangelo, who reads Donnie's goodbye note. Poor guy's probably having flashbacks to the last time the Turtles were drifting apart in Northhampton; only this time, he isn't sure how to fix it.
Issue 103 has Mikey finally reacting to something... namely, his pet cat Klunk is missing because the door was accidentally left open. Leo helps him look for Klunk but they are not having any luck. After the deaths of Splinter and Slash, as well as that if his mother in his previous life, the prospect of losing another loved one causes Mikey to break down in tears, with Leo firmly hugging his brother to try to comfort him.
When Jennika calls out Raph on his bad attitude and shunning everyone away (including her, for she had hoped he and his brothers would be able to help her cope with her mutation) and reminding him that other people loved Splinter too, including herself, Raph insults her fiercely, saying that Splinter only took her in because he felt sorry for her, and that now that Splinter's gone, nobody cares about her nor wants her around. As he takes his leave, Jennika visibly tears up in sadness.
Issue 111, oof. Mona Lisa finally gets to call her parents for the first time since mutating. They do a video call, but the minute her parents see what she's become, they immediately hang up. Poor girl breaks down in tears, can you blame her?
Alopex breaking down upon Shredder's return, then her quitting the Splinter clan after she learns that they will accept his help.
Issue 8 of The Armageddon Game has the Rat King kill his siblings one by one, and we see Kitsune knocked to the ground, unmoving. Saki cradles her gently and begs her to wake up. It's small, but it's a raw moment of vulnerability from The Shredder of all people. Given how he promised to find his way back to her even in death, it's obvious just how much Saki truly cares for Kitsune, and even through his mask, he looks terrified at the thought of losing her.
Even though she does wakes up, Saki still does end up losing Kitsune, with her pulling a Heroic Sacrifice to take the Rat King with her. While it's unlikely she's gone for good, given her established Resurrective Immortality, it's clear that her loss has hit Saki hard.
