Handsome Jack's entire character arc. You have this friendly programmer, trying to be a hero and save an entire planet, and he just slowly gets darker and darker. And when Lilith maims him with the Vault Key, you know that he will never be that friendly programmer ever again. What Athena says during the fight against RK5 nails down what Jack is about to become:
Athena:(under her breath) He's losing it.
Of course, knowing what he's already done to Angel makes it worse, because it means the friendly programmer wasn't quite as heroic as he liked to portray himself as.
It's a quiet moment, but after Moxxi overloads the Eye in an attempt to kill Jack, you can go back to the office and see that the picture of a smiling Angel on his desk is now face down. It demonstrates his choices quite clearly.
Nisha's backstory. An abusive mother, a cowardly father, a dog she loved so dearly turned against her by the very same monster who's been haunting her entire life...no wonder she's such a sadist.
She also got a phobia of puppies from said experience. Which is why she murdered Brick's dog before Borderlands 2.
What's worse is that she was born in bandit country-definitely not a pleasant place to live. This may be where she got her love of killing people from, and given that most bandits are terrible people, she got her Jerkass attitude from her mother.
The side-quest Tales from Elpis is about the Vault Hunters fetching and hearing about Janey Springs old entertainingly bad ECHO childrens stories. The quest largely comedic all round with the exception of what she says before we get the second ECHO. Its the one point in the story where Springs optimistic persona falters.
To make matters worse, there are bloodstains all over the room when you open the door to the camp. And a torn up teddy bear.
The Merriff's betrayal, and subsequent back shooting. Jack had actually said he was willing to let him go, and yet the betrayal that followed is... heart-breaking. This is the moment that will define Jack for years to come. The lesson Jack learns is that if you show mercy to anyone, you will inevitably be betrayed. Made worse when you listen to the Merriff's recordings. He honestly regretted everything wrong he'd done...
Skipper/Felicity's ultimate fate. The future looked so bright, and then she ends up being forced into a Constructor body, has her memory wiped, and has to be effectively killed. Jack even seems to consider the idea of copying her instead, but since it would take days, Jack says they can't afford to wait. Since this is during Jack's Start of Darkness, he still has enough sanity that he sounds genuinely apologetic.
Sadly, even Jack's seeming remorse feels hollow. He quickly gets over whatever feelings of conflict he may have had as the fight goes on, reverting to his usual tone and is more impressed by Felicity's combat abilities than he feels guilty.
What makes it worse is that both Athena and Gladstone agree with this course of action, albeit reluctantly. As the subtitle says; 'If only Elpis had more time.'
What can also make it worse if you're playing as Claptrap. After Felicity screws up and accidentally activates a pair of turrets that immediately begin attacking the Vault Hunters, Claptrap has evidently fallen in love with her and wants her to marry him. Poor robot can't catch a break.
Claptrap: From one artificial intelligence to another, I appreciate your respect and OH GOD YOU'RE SO WONDERFUL, CAN WE GET ROBOT MARRIED?
The ECHO logs detailing Athena's backstory, as recorded by General Knoxx. He talks about Athena and how she seems nice enough and he learns about how Athena was planning to meet up with her sister (Jess) and escape Pandora together. He then implores his superiors not to 'screw her over'. His next ECHO has him calling them out on ordering a hit on the village Jess lives in (knowing full well she lives there) and how Athena wasn't even aware she was killing her sister because she was ordered to use only thermal goggles during the operation. After realising what she'd done, she apparently 'got a little stabby', which is the most we hear about how it affected her. Knowing the full extent of the situation kind of makes an already tragic backstory even worse.
Even if we already knew it was going to happen, that image of Jack trying to destroy Claptrap, ripping out his stair-climbing wheel and shooting him. Love him or hate him, Claptrap never had the option of rebelling and did nothing but help Jack, but that didn't protect him.
The sidequest "Don't Shoot the Messenger": After comedically receiving an ECHO and instructions from several people, you finally deliver an ECHO recorder to a woman in Concordia and the side quest goes from a light-hearted side quest to the mother of all Mood Whiplash moments. You've just delivered a post-mortem message from Colonel Tungsteena Zarpedon to her daughter, Britannia, who she has been estranged from. Zarpedon explains that by the time her daughter receives the ECHO, her and most of her troops will be dead and that she needs to flee Elpis immediately. It's when Zarpedon states she always loved her daughter and has regrets missing her grow but her mission was for the good of the universe and instructs her daughter to live and lock and load that the Tear Jerker moment comes to completion. A fantastic and simple way of making one of the main villains of the game a humanized and sympathetic character, despite the terrible deeds Zarpedon has done.
Zarpedon: Beloved daughter... I didn't die that terrible day, but was instead taken by Elpis, along with most of my soldiers. There, entombed beneath the ground, I found a higher calling. Every day I wonder if giving you up was the right choice — the universe in exchange for the one person I love. But my actions protect the universe and therefore protect you. This ECHO's my backup plan. I've missed watching you grow and get the sense this mission won't be one I come back from. I'm truly sorry. Listen to your old mom one last time: bad things are about to happen, and you must flee Elpis immediately or you will die. Know that I was always proud of you, that I didn't want this for us and that we'll meet again. Lock and load honey — it's a beautiful, terrible universe out there.
The entire story of Claptrap in the game. He has his memory erased of the events of the previous game, only to be re-purposed by Jack into the Fragtrap. Claptrap proceeds to become a Vault Hunter who can climb stairs and kick ass. Jack, however, becomes so annoyed with the Claptrap line he destroys all of them before dismantling his creation—leaving him for dead. This, despite the fact Claptrap helped put him in power. The saddest part? Claptrap thinks Jack and the Vault Hunters are his best friends in the world until this point.
As the Vault Hunters chase Shadowtrap through the Subconscious, Claptrap's Consciousness tries to remember what he was going to tell them about Shadowtrap, only to forget a few seconds later. The Vault Hunters lose their patience and tell him to shut up, causing Claptrap's Consciousness to finally snap and express his pent-up outrage:
Claptrap's Consciousness: WHY are you ALWAYS so mean to me? EVERYONE is ALWAYS SO MEAN! All I've ever done is try to help! I know I mess up, and I'm 10 to the power of 100 of SORRY about it — but if you can't see that, and can't take my good intentions for what they are, then maybe you don't deserve anything good to ever happen to you! In fact, I'M OUTTA HERE! Ah. I can't leave — I live here. But I CAN leave you!
Claptastic Voyage's climactic scene: Jack outright murders Claptrap while Wilhelm and Nisha sadistically chuckle and give a high-five in the background, and Athena watches quietly. Neither of them lifted a finger to help him, and all of them thought (to varying degrees) that he was an annoying waste of time. This is also preceded by shots of every Claptrap unit in the game short-circuiting and dying, from the Customs Claptrap to HAL Claptrap the Scav Claptrap, finishing up with the climatic scene mentioned before.
Although the closing scene of the DLC has Athena saying that's not exactly what happened and that she had no idea Jack was going to kill off Claptrap's product line, so that part may have been Claptrap embellishing.
Claptrap's also been the most hated character, in-universe, in the series up to this point. Almost nobody likes him-from the Vault Hunters themselves, to bandits, to all the NPCs that can speak. Sure, he's liked by Angel and Steve and Janey and possibly Karima, but pretty much the entire population of Pandora and Elpis despise him and would happily see him die. And if he did die, nobody would give a damn.
During said montage of dying Clap-trap units, B4R-BOT is shown at Moxxie's bar, and begins to stutter, spark, and topple over. While this, happens Moxxie can be seen clasping her hands over her mouth with a look of horrified shock. At the end of the montage Athena (who if you play as her gets to know Claptrap on a more personal level) turns away in disgust. This means that not everybody hates Claptraps as much as they let on, which can make the ending less of a tearjerker or more of a tearjerker depending on how you look at it.
The Handsome AI mission sheds some light on Jack's childhood. It's... not pleasant. His mother passed him off to her own mother when his dad died, and his grandmother regularly beat him, and murdered his cat when he didn't make his bed. Made worse by the fact that Jack dismisses this as 'usual stuff' so nonchalantly in a bored tone, like it's a normal, everyday thing for everybody. It goes to show that even before the Pre-Sequel started, Jack had a warped perspective of how things are and should be.
Pickle's ECHO Logs in the Claptastic Voyage DLC. Turns out the reason he wanted to get onto the Bosun's ship so badly wasn't to steal the tech onboard, but to recover his parents' ashes. Makes you feel sorry for the little guy.
The Claptastic Voyage DLC gives a view into Claptrap's mind and his self-image. It's... not pleasant, with his failures compounded by the fact that he genuinely wants to help but can't. He's also fully, painfully aware of how much everyone else hates him, to the point that he suspects that anyone who does seem to tolerate him (such as Janey Springs) is just lying to avoid hurting his feelings.
The entire Overlook section of the DLC. It starts out funny before Mood Whiplash sets in; Overlook seems to worship Claptrap as the greatest thing ever, singing songs and putting up decorations in his honor. These are quickly revealed as false memories, covering up what really happened. Claptrap's consciousness tries to get you to leave them alone, which makes it initially seem like the events were embarrassing for him, but the reality is that they were tragic; Claptrap tried to help with a tournament festival, but set up high-grade explosives instead of fireworks, killing about half the town in the process. Despite this, Karima still trusts him to deliver medical supplies to a makeshift hospital, in the hopes that people will forgive him if they see his heart is in the right place. He accidentally starts a fire, killing more people, and Karima's husband is among them. And while the explosives were an idiotic decision on the robot's part, the fire was a honest bit of klutziness that could happen to anyone... and that's the story of how Claptrap got run out of Overlook, and why the town has so few surviving members when the Vault Hunters in Borderlands 2 show up.
Once you reach his subconscious, he asks you to help him find Hope and Self Esteem, which would help him go anywhere. When you reach them, they've been corrupted by Jack into Despair and Self-Loathing.
Claptastic Voyage has a side mission that follows the hilarious hi-jinks of Claptrap's superego, as he endeavors to save a Damsel in Distress from a moustache twirling villain, which quickly whiplashes when the 'damsel' turns out to be a representation of Felicity Rampant, who insists that Super-Ego-Trap isn't the hero of the story that he thinks he is, but the villain. Claptrap's superego briefly tries to own his villain role before breaking down about how he just wanted to save Felicity and doesn't understand what he did wrong. This could easily be interpreted as Claptrap being unable to reconcile the heroic image of himself as a Vault Hunter with the extreme guilt he feels over Felicity's fate.
5UP4-3G0-TP: I only wanted to save her... I don't know what I did wrong.
The end of the Claptastic Voyage storyline. Jack uses the H-Source to destroy all Claptraps. Complete with slow-motion footage of every single memorable Claptrap across the Presequel dying as they are permanently shut down. It then ends with Handsome Jack gunning down Claptrap himself in his office while his "friends" Nisha and Wilhelm laugh and high-five, before he's dumped in the frozen tundra with the rest of the destroyed Claptraps. In the end, it's only Shadowtrap himself that keeps Claptrap operational despite the damage until Sir Hammerlock finds him.
Claptrap's Subconscious holds a surprising amount of insight when describing the Vault Hunters when they first enter:
The Theme to the DLC, which is sung from Claptrap's perspective of the events. And like everything else in the DLC, it's a huge turnaround from the other vocalized songs. Based on lyrics alone, Claptrap is saying that he cannot be The Atoner despite being apologetic for the catastrophes he committed, and that he wants to die. Made particularly horrible when played alongside the picture of Jack shooting Claptrap and tearing out his wheel during the credits.
Now can feel the gravity I believe the real reality I've caused so much brutality Pain at full capacity What have I done What went wrong
Nothing more to give I've lost the will to live So ashamed of what I did No way they can forgive
I'm sorry for the lives that I have torn I'm sorry for the lives that I destroyed
Nothing more to give I've lost the will to live So ashamed of what I did No way they can forgive.
When told during the New Game Plus, Claptrap shares some rather meaningful words at the end about what he learned from the experience, only for everyone present to yell at him to shut up. Some consider it a pretty inappropriate moment to bring up a mean-spirited Running Gag from the last game.
During the last Boss Fight Shadowtrap reveals through the mouths of Zed, Lilith, and Tannis, that he has seen everything through Claptrap, and calls them out on everything they did, working for someone as obviously awful as Jack.
Shadowtrap's rant after seeing the hologram is similar to a sibling who was neglected by said father, and has now become excessively bitter and angry.
One of the first rooms in Claptrap's Subconscious level is full of teddy bears and children's blocks, which at first feel like a representation of Claptrap's child-like personality. Then you might realize that the blocks spell words like "SORRY", "ASHAMED" and "HUMILIATED". The whole DLC turns very uncomfortable once you realize it's representing a mind suffering from profound mental trauma and crushing emotional abuse that literally isn't programmed to properly express. When in Borderlands 2 Claptrap says that despite his cheerful tone he's actually quite depressed he isn't kidding.