The Lost Legion Eternals are soldiers of Zarpedon who use Eridian technology excessively. They can also "ascend," gaining a new class type. One of those types has energy wings that look suspiciously like a Siren's. They can even manifest the same abilities as existing Sirens, such as an "Eternal Phasewalker" and "Phaselock Eternals". Combine with the Guardians allowing Lilith into the Vault, some of the Siren/Eridium connections from the last game, and it's no wonder that the Alien took a special interest in Lilith at the end of the game (enough to keep her from executing a valuable ally). Sirens have some connection to the Eridians, and the Alien wants to keep her safe.
One sidequest in Crisis Scar; "The Empty Billabong", seems like run-of-the-mill Borderlands insanity, until you finish the game. Jolly Swagman's ECHO describes a "giant empty billabong, with purple lights shooting out of it, and the silent prayers of an ancient people ringing in its depths", one can just attribute this to his usual crazy self as described by Peepot, seeing as it makes absolutely no sense. That is until you get to Tycho's Ribs and its deepest level, Eleseer. It's exactly as Jolly Swagman described it; giant empty location with purple lights and the silent prayers of an ancient people ringing within. Clever foreshadowing hidden in drunken shenanigans and humour, typical Borderlands.
This also suggests that Swagman's rambling is just as unintelligible In-Universe; he straight up says what he saw was in Vorago Solitude, but Jack still needs to figure out that location later in the story. That means neither Jack nor any of the Vault Hunters are able to make heads or tails out of it.
In one sidequest on Helios, Jack has you collect ECHO's regarding you and the other Vault Hunters, saying that he doesn't want the Lost Legion to find them and take vengeance on you once this is all over. But when you listen to them, there's nothing really incriminating in them besides your names, which the Legion probably already knew. The real reason he needed them was because Angel's in them, and he was trying to keep her secret.
Notice how Moxxi doesn't use any sexual innuendos when she's manipulating Jack and his team into destroying the Eye of Helios. The only time she drops those is when she's being deathly serious and needs to focus.
Janey Springs offers you a quest to retrieve a grinder, mentioning that they are 'useful for other stuff.' What does she mean by this? Janey is a black market dealer, and in the Borderlands universe, guns come in much more distinct and varied shapes, sizes, and colors. By grinding three stolen, easily identified guns into one mashed-together one that doesn't match any of those three descriptions, she can essentially launder weapons.
Why is the Raid Boss simply a tougher version of the Final Boss? Because Athena's making that part of the story up and she doesn't have much imagination, so she sticks with the strongest enemy she's ever fought, only tougher.
Remember how Claptrap, who is in fact the very first Claptrap you meet in 1 (and at that point had not gained a personality of his own yet), easily broke down after a few shots from a bandit drive by? And as we have seen throughout the rest of both the original game as well as The Pre-Sequel!, other Claptraps are still just as easily destroyed. How is it then that in Borderlands 2 Claptrap has survived having his eye ripped off, blown up at nigh-point blank range by a battleship's cannon, and being kicked repeatedly, all in the span of a couple of hours? Even if he lost all his combat skills and stair-climbing protocols, which are software, he still kept his MUCH sturdier chassis from when he was the Fragtrap.
On a side note, him having once been the Fragtrap is a good explanation of why he has a gun cabinet in his home despite being unable to fight anymore.
On the topic of Claptrap, recall that he was expecting to be welcomed into Sanctuary with much celebration? This may not have been unfounded bragging, considering he really was a Vault Hunter in his own right. Then again, no one but himself, Jack (who might have deemed him as an actual threat anyway), and some quest givers actually saw him with that kind of respect or even know he could kick as much ass as a Vault Hunter; even in-game, Dahl soldiers who spot him will call him out as an "easy kill" (before getting their faces blown off of course).
Also, recall how Claptrap was convinced that Jack was planning to destroy him in 2, when he was really just targeting the Vault Hunters on Pandora? Since Claptrap is a former Vault Hunter and Jack already tried to kill him once (as seen in the credits of the Pre-Sequel!), it makes sense that Claptrap would think Jack would want to finish the job and that he's a target along with the other Vault Hunters. Claptastic Voyage takes it even further with how far Jack went to use the H-Source to destroy all Claptraps. He even personally gunned down Claptrap once his use finally ran out... the same treatment that all Vault Hunters get in 2 (i.e. the train being a trap for Vault Hunters, as seen in the intro).
Claptastic Voyage offers a grimmer possibility; Claptrap once lived in Overlook, and his attempts to help the people there just ended up causing disaster and him being universally despised. But when you view his memory of the town, everyone loves and celebrates him. He's so desperate for love and acceptance that he created a whole denial subroutine to hide the truth, even from himself. Well, if anything, the people of Sanctuary have even more reason to resent Claptrap than those in Overlook; he's partially responsible for the rise of the genocidal madman who's out to destroy them. As before, Claptrap is in total denial about this, convincing himself he'll be adored and celebrated instead. At the very least, no one seems to actively hold it against him this time; Moxxi, Roland, and Lilith are the only ones who know about the events of TPS, they are probably aware he couldn't violate his programming as a Hyperion robot, they already tried to kill him once, and so at least it's nothing personal.
How did Wilhelm almost kill the Original Vault Hunters and burn New Haven to the ground without taking a scratch? Saint was there.
Claptrap's VAULTHUNTER.EXE ability is able to near-perfectly mimic the action skills of all the second-generation Vault Hunters (his version of Zer0's Decepti0n is even superior to the original in that attacking doesn't cause him to uncloak)... except Maya the Siren's. Claptrap can't Phaselock, so he instead imitates Maya's Blight Phoenix kill-skill. This is in keeping with Sirens being absolutely unique in the Borderlands universe. As amazing as the technology built into Claptrap is, it can't mimic a Siren's primary ability because absolutely nothing in-universe can do so.
Back in the second game, Handsome Jack screaming at Angel that "All the bandits I've killed, all the people I've manipulated, all of it was to protect you!" comes off as a desperate father trying to convince his daughter to not commit suicide... but as The Pre-Sequel shows, no, that's all one big lie. Everything he's done over the course of Borderlands 2 was just to get revenge on Lilith, Roland, and Moxxi for trying to stop him in the first place. He's just a desperate, lying bastard during the course of the whole game.
Claptrap being one of Handsome Jack's enforcers explains why most of the characters he invited didn't attend his birthday party in the second game; Moxxi felt awkward or guilty about the entire "tried-to-kill-him" business and probably forbade Scooter from going.
Why does Lilith have such a psychotic overreaction to Athena stating they're not so different? It's because Lilith betrayed Jack and destroyed his face. Which causes his Roaring Rampage of Revenge/War with the Crimson Raiders/Bloody takeover of Pandora. Lilith's feeling guilty she caused so much damage and is projecting on Athena.
Why did the Hyperion Board of Directors choose to make Handsome Jack their CEO and sign over their shares? Borderlands 2 leaves that inexplicable, implying possible threats. Here, however, Jack saves Helios Station/Elpis and personally defeats an army with almost no resources. He must look like a big hero. Tassiter is the only one who knows how much of that was luck, the Vault Hunters in Jack's employ, and criminal behavior, and by the end of TPS he gets killed by Jack.
Jack's character development now makes a great deal more sense with his Abusive Parents and Freudian Excuse working well with his later behavior. Jack was tortured by his grandmother growing up. Later Jack becomes devoted to having power and the approval he was denied. It also explains why betrayal stings him so bad as he overcompensates for his lack of early good relationships. Not to mention how he treats his own child.
Why do so many Power Loaders have weird-weird quirks in Borderlands 2 like collecting porn or trying to become human? Because they were created by Felicity.
The Guardian Sentinel is sort of a strange final boss to the game, not having much to do with the main plot which was resolved after the death of Colonel Zarpedon. It's also an emotionless, mechanical, and un-characterized creature with no personal connection to the players. Then, after you finish, you realize the main villain of the game is Jack and you just helped him come into existence.
Captain Chef is Played for Laughs, being a pseudo-19th century British explorer in the 56th century. However, most of his comments relate to how the natives (Elpian space-travelers) should be grateful for the fact he's coming to civilize them by claiming their world. Also, that they are silly for objecting to being killed with "superior advanced weaponry." The thing is, this summarizes Jack's worldview.
And like Jack, Chef hires your character to do all the work, mowing down locals while he mostly stands there and provides commentary, then takes all the credit for himself.
During the mission where you have to rescue three scientists in Helios R&D, there are several indications that Gladstone is right and there is a traitor; it's the third scientist you visit. The third is working on stealth technology, and it's difficult to miss that the Lost Legion scouts that you've been encountering on Helios are already equipped with that exact technology that hasn't been released for Hyperion's own soldiers. When the other two scientists send you on minor errands in areas that are incidentally dangerous, the third scientist's seemingly minor errand leads you directly into an encounter with a miniboss Stalker - an enemy significantly more powerful then anything else you've encountered in this area. He gives you no warning of the miniboss until it's right on top of you, but it's clear that he knows exactly what you're walking into - he claims that it's the stalker that ate his keycard and so would already be aware that it was hiding in his workspace. Furthermore, its name indicates it's an experiment he was working on, so he's likely aware of its abilities and resilience as well. Doubles as brilliance on a meta level, as the attempted betrayal is disguised as the end-of-dungeon boss to the player. Thus, Jack's airlock murdering was at least 1/3 justified.
Also, look at what he's wearing. It's a jetpack just like the Lost Legion soldiers equip.
Wilhelm, Athena, Nisha, and Claptrap all get a good look at how Handsome Jack rewards traitors while considering the people underneath him expendable. All of them betray Jack by helping Tassiter gather information about his activities. It makes you wonder how much Jack knew since he ends up betraying half of them in the end. Becomes a Karmic Death for Wilhelm given his betrayal of Felicity with Claptrap getting equally stomped on. While Nisha dies for reasons not directly related to Jack, Athena gets away without consequence; appropriately, this is because she was the only one whose betrayal of Jack by helping Tassiter wasn't for selfish reasons but to protect her remaining family.
The song "Come With Me Now" is used in a pre-release trailer. It's about a man who is so evil, the Devil refuses to buy his soul. Now, think about what happens to Jack over the course of the game...
The Meriff's revolver only being able to fire 2 shots when he tries to shoot Jack in the back seems odd, except the first game actually did have revolvers (usually high-damage Jakobs revolvers) that only hold 2 bullets. If he had been using a Scav pistol, or even a Jakobs that held 6 rounds, it's likely the entirety of Borderlands 2could have been avoided.
At the end of the game, Lilith only strikes Jack once before disappearing into a portal. Why didn't she stick around to kill him? Because she was Phasewalking into the alternate dimension within the strange crystal, and when Lilith Phasewalks, she only gets one punch before she reverts back to normal reality. She Phasewalked in, punched the Vault artifact, drove its energy into Jack's face, and then had to leave immediately afterward without being able to stick around and finish him off. Staying would have her have to fight six Vault Hunters at once. Attempting to go back in a second time would have her entering an area with the same six heavily-armed Vault Hunters who were now ready for an attack and riddle her with bullets.
The Sentinel, while not necessarily of importance to the plot, has masks over its 3 faces that give it a youthful and handsome appearance-shoot them off and you'll find a hideous alien skull. Clever Foreshadowing for what happens to Jack after the boss battle.
In Borderlands 2, why was Hyperion so desperate to get the Wave-Motion Gun that TK Baha designed? The Eye of Helios turned out to be a WMG controlled by the Eye of the Destroyer, which was soon destroyed by Moxxi, Roland and Lilith. That gun is the best shot for recreating a weapon on par with the Eye, this time without needing an eldritch abomination's eye.
Jack seems to have a limited supply of Constructors available throughout Borderlands 2. He only ever throws a couple at a time at the Vault Hunters when several dozen such units working in unison might overwhelm the Vault Hunters. This game actually gives a hint as to why; because it takes a couple of days to fully copy the AI that runs each Constructor, which are in effect a stripped-down Felicity. This forces a bottleneck on how many Constructors Jack can actually have active at any time, exacerbated by the fact that the Vault Hunters keep blowing them up.
There's a ton of irony and symbolism surrounding Jack's mask.
According to Moxxi, the real Jack, beneath his veneer of heroism and selflessness, is a complete psychopath. The course of the game is the gradual descent of Jack, showing how he reacts when presented with dark choices and ugly decisions. We see his willingness to kill and deface the memory of his enemies after they die, his willingness to sacrifice his own loyal employees because of a vague threat to himself, and his overwhelming greed, which comes to dominate him as you get closer and closer to the Vault (and incidentally, made him completely disregard Zarpedon's warnings about the Vaults). And at the very end, after Lilith scars him, we finally see the real man underneath it all. It's rather ironic that at the very moment we see the real Handsome Jack, previously hidden beneath the metaphorical mask of heroism, he's put on his physical mask to hide his scars.
It's also rather telling that Nisha is completely uninterested in Jack while he's acting like a hero. She has no interest in the mask. But as his facade is torn away piece by piece, she becomes gradually more attracted to him, until she fully falls for the psychopath underneath it all. It's the point where Jack puts on his physical mask and completely discards all shreds of his heroic tendencies that she truly loves him and helps him in his rise to power (although she doesn't share his grand vision.)
How are constructors in Borderlands 2 able to create fire shockwaves? They're all equipped with incendiary Oz kits.
The whole Convection Shmonvection problem could easily be resolved by one thing - you always find lava in areas without an atmosphere, meaning convection is impossible.
One of the major plotholes in Borderlands 2 was how after Jack captures Lilith, he doesn't mortar Sanctuary despite the only reason he avoided doing so (Lilith being able to teleport it away) being gone. However, this game answers why; Jack never really cared about Sanctuary's destruction, he wanted Lilith to suffer for what she did to him. And his obsession with the Warrior despite already having an army that can easily sweep Pandora? It was the last thing in his mind when Lilith punched the Vault database into his face.
Given that Hammerlock was the one that introduced the Threshers to Pandora during the events of this game, this means that Terramorphous the Invincible is actually only about 5 years old due to the timeskip between Borderlands 1 and 2 being roughly 5 years.
Confused how in the ending of Claptastic Voyage, Claptrap survived the destruction of his product line and had to be taken out by Jack personally? Don't be; as one of the loading screen tips points out, Claptrap's combat protocols changed his model designation to FR4G-TP, but the kill signal was targeting CL4P-TP units.
One of the first things Jack does upon becoming Hyperion's CEO is set every CL4P-TP unit to self-destruct, followed by shooting the FR4G-TP himself. Fast-forward to Borderlands 2, where we're told Jack sacked New Haven with hardly any effort at all, leaving the Vault Hunters and their allies from Borderlands 1 scrambling to evacuate to Sanctuary. Go back and play Borderlands 1. What do you see maintaining and operating the gates and serving as lookouts around all civilized areas? CL4P-TP units. They may have been buggy, quirky, and annoying, but Claptraps were an essential part of the security systems for anyone trying to maintain civilization on Pandora. Without them, there's no security or advance warning of threats.
It's mentioned on a couple of occasions that most of the air on Elpis "smells like farts" which may come across as Toilet Humor or a joke about how many times the air has been recycled. Then you remember that Elpis has vast deposits of frozen methane - which smells like rotten eggs.
Felicity is a female A.I in a robot body, forced to create smaller robots. It's a literal Baby Factory.
For all his "heroic" trappings, Jack is directly responsible for starting the war that the Watcher is warning of. His greed to take control of the Vault and its riches, and then later the Warrior, is pretty much triggering whatever horrible apocalypse that Zarpedon was trying to avert, and worst of all, Jack deliberately ignored all of Zarpedon's warnings, dismissing her as crazy or insane. If he'd actually stopped for a moment to think and ask Zarpedon why she was doing what she was doing, and listened her final warning rather than shooting her dead before she could tell him what dangers the Vault contained, he would have known what he was going to unleash. But his greed blinded him to that; as far as he was concerned, Zarpedon was an obstacle to his goal, and he'd make up any excuse he could to justify ignoring her. And because of that greed, he unknowingly started a war that might endanger the entire universe. It's rather ironic that the man who considered himself the savior of Elpis and Pandora was actually directly responsible for triggering a massive war that threatens to destroy everything.
Janey and the Kraggons:
Janey had a female significant other who was killed by a Kraggon. One of the ECHO recordings the player retrieves for her during a sidequest is a story about two Kraggons, one of which is a child, and the other revealed to be the same 'Flamey' mentioned before during the quest. The 'song' states that Flamey 'tore up a two legger pretty bad' which we already know to be Janey from a previous recording. The song also mentions that 'baby killed another'. During dialogue over the course of the quest, Janey will mention Kraggons before saying 'They killed her. They killed my...' but stops herself short. In Australia, there was a particularly famous trial in which a woman was accused of murdering her daughter during a camping trip, but claimed in her defense that dingos had eaten her child. She was right.
Alternately, for added horrible, the contents of the raided camp include a teddy bear and a small camp bed, rather implying, as does the Lindsey Chamberlain reference, that the person killed was actually Janey's daughter. Try not to think of how an attractive lesbian living in a remote area surrounded by bandits might wind up pregnant... So yeah, added horrible.
Felicity doesn't want to be a soldier, so she offers to make a copy of herself. You'd think the copy would feel the same way...
This gets worse: since the Fridge Horror below mentions that the robot army wasn't for Helios, Jack COULD'VE had all the time in the world to copy the AI. He just blatantly disregards her.
The various Claptraps we meet: Hal Claptrap, Dalek Claptrap, Shodan Claptrap, Police Claptrap, the Claptrap who opens Jack's office, R2-D2 Claptrap, and all the others are all destroyed by Handsome Jack upon his rise to power. This is especially egregious as many of them assist him in his rise to power. Jack's reasons for doing so? He can't stand their quirky personalities, and one or two of them mildly inconvenienced him a couple times. Not only that, but all of the Vault Hunters in The Pre-Sequel! were directly responsible for Jack being able to wipe out the Claptraps by retrieving the H-Source. Athena herself is utterly and completely disgusted by this revelation.
By the end of the adventure, you realize Roland, Moxxi, and Lilith's failure to kill Jack followed by a second subsequent attempt resulted in the CEO of Hyperion becoming obsessed with destroying them. They managed to destroy the Eye of Helios and keep most of the Eridian's knowledge out of his head, but still ended up helping him become the most powerful man on Pandora. They may not be responsible for turning him into a monster since Moxxi implies he always was one but they were responsible for turning his wrath toward Pandora itself.
When you go to investigate the sick workers quarantined within Helios, you end up getting infected yourself. However, it turns out that there's an incredibly easy way to cure the infection, demonstrated by you during the mission: leave the area with the disease to expose the mind worms to the vacuum of space. Which means that the quarantine that Jack imposed to contain the infection was not only unnecessary, but directly responsible for the workers' degeneration to an incurable state. Though he had no way of knowing it, if Jack had just let all the workers escape the area, no one would have been infected and become Rats.
Jack makes a big, big deal about getting a hold of a robot army. You do a lot of missions for it, and wipe Felicity's personality to expedite the process, because Jack claims that Elpis won't survive long enough to copy Felicity. When you finally get them? The attack on the Helios Station is mainly done by the Vault Hunters, who Fast Travel in with no robot support. The only kind of robots that help the Vault Hunters are worker units already on the Station, and that's because Jack uploads a program to convert them into fighters. Jack didn't need Felicity for the attack on Helios. He needed it for his dominance of Pandora.
Janey Springs has a bit of an Impossible Hourglass Figure going on. Par for the course with stylized character design, right? Then remember she was stuck in a crashed ship surrounded by magma monsters and bloodthirsty bandits for months, and if you look closely at her midriff you can what seem to be her ribs and pelvis. She was probably starving out there.
Listen to Nisha's ECHO logs again. She mentions that her puppy got infected with something like rabies, then managed to bite her. Now, think about how she used to be as a kid based on her old logs, and what kind of person she now is.
Claptastic Voyage takes place in Claptrap's mind, and as such we see representations of those he's close to, like Brick, Pickle, and Springs. At the same time we see that he thinks they all secretly hate him. That's bad enough, but where are the characters that are canonically supposed to have genuine love and friendship for him, Tate/Asha and Steve? Asha is from a possibly non- canon Broad Strokes adaptation of the first game, sure, but Steve is supposed to be canon. Remember that Claptastic is him telling the story, not a "live" event, so if he's as depressed as he says he is, it would make sense that he's disregarding them entirely.
Moxxi threatens to have you killed if you tell anyone else she used to be a Hodunk after you stumble upon her in her mechanic outfit and not talking in her usual accent. While this seems pretty excessive at first, keep in mind basically everyone hates bandits (including the Hodunks), and considers them Acceptable Targets. If they find out she used to be a bandit they could well have her executed.