Beware of Unmarked Spoiler ahead!

Fridge Brilliance:

Orange is a common color for protective eyewear in marksmanship, since it helps to sharpen contrast and depth. So Vash's orange shades are both functional and fashionable.
- Another possible function of Vash's shades is to hide the Plant markings that appear in his eyes under bright light, as seen in episode 8.
The decision to make it so that Meryl's occupation from the get-go is that of a reporter instead of an insurance claim agent has a certain brilliance to it, as while both jobs give her a reason to tail Vash, the job of a reporter puts her in a position where she can help clear misconceptions about Vash, who the world hunts down as a Wanted fugitive despite the fact he wants nothing more than to just help people. Meryl is also the closest thing to a Point of View character Trigun has, so her being a reporter is fitting because it means she can chronicle Vash's story for the masses, instead of just writing internal memos for the insurance society.
Legato, Zazie, and Elendira all have asymmetrical hairstyles that has the right side longer than the left. Who else had a similar style? Vash when he was a kid. Not only does this show that Knives really, really misses his brother, but it also shows his inability to let go of the past and accept the changes in their relationship. In Elendira's case, her being a partial clone of Knives makes it seem like he's trying to make a Replacement Goldfish. Also, a closer inspection of Knives's right upper arm as a teen in episode 9 shows it's wrapped in bandages. It seems to be an area where blood is usually drawn, and Knives rarely if ever gets injured. So it's likely that Conrad's experimentations in Plant cloning and hybridisation started after Knives threatened Conrad to join his side.
- A closer look at Elendira's eyelashes shows they are identical to the eyelashes of the Plants, another hint at her being a Plant-derived clone.
Wolfwood is an "undertaker" rather than a priest this time around because a priest ministers to the living while an undertaker prepares the dead, and his mission is to ensure Vash is delivered safely to what might as well be his death.
The Plants in the manga were originally encased in lightbulbs. Here, they still keep the light-bulb motif, but just in their default form. Now they are more literal representations of the energy the people on Noman's Land need to survive.
Without being told where to go, Vash and Knives can easily find the Plants location if they happen to be in their vicinity. Even as children, Vash and Knives could hear the other Plants "speak" to them since they are Independent Plants.

Episode 1: Noman's Land

Zazie claims that the worms have inhabited No Man's Land for far longer than the humans have. As Vash and Nai's escape pod falls towards the planet, you can see specks of glowing green haze on the planet's surface, which can also be seen during episode 4. These are likely a swarm of bugs, which bolster's Zazie's words.
The car stops dead due to running out of battery, which Meryl quietly admits to forgetting. Since there's no fossil fuels for gasoline on a desolate sand planet, running off Plant charged batteries would be the next solution.
Aside from her naivety, Meryl wanting to clear Vash's name before possibly turning him over to the police aligns with her beliefs. A quick glance at her resume that Roberto half-heartedly perused, states Meryl wishes to be a reporter for humanitarian purposes, and that she believes in the good of others. So it makes more sense why she wouldn't buy into the magazine's story of Vash the Stampede, the "Humanoid Typhoon" and laughs at his caricature.
Meryl: (giggling) Real people aren't such caricatures.
With a hint of sadness to it, Vash seems very close with Rosa - a mother with a young son and another child on the way. It's likely because Rosa's maternal side reminds him so much of Rem, who he still mourns for 150 years after she sacrificed herself to save the people on the ships. Funnily enough, the way part of Rosa's hair falls on the right side of her face is reflective to Rem's hairstyle.
Roberto notes that Meryl comes from not only a very high standing school, but extra material reveals she also comes from wealth. This explains her not understanding that a place as downtrodden as Jeneora Rock would not have the resources to keep itself or even its guests going. Hence why Roberto defaults to asking for whiskey instead of water - likely gathering before Meryl even does that the town is on hard times. He's right when he says that Meryl still has a lot to learn.
After the July police capture Vash, they declare they're taking him back to July. Vash's face gives way to a small Oh, Crap! expression. He likely knows Knives is at July and that's the last place, or person he ever needs to see.
- Rosa is told by Chuck Lee that Vash's bounty of 6 million double dollars is about the price to fix their current dying Plant. Vash is later revealed to be an Independent Plant. It should also be noted that it's likely Conrad and Knives were the ones who set up the bounty, with Vash's wanted poster specifically asking for Vash to be brought in "alive". After Knives' incineration in the season 1 finale and the destruction of July, there is no one stopping Vash's bounty from turning into "Dead or alive".
A hint towards how much better of July is compared to Jeneora Rock, is the fact that the other MP's are readily placing bets on Vash and their captain. Tossing out up to fifteen thousand double dollars freely. Whereas Jeneora Rock's inhabitants are barely scraping by and have no means of buying a new Plant. We later find out July is the water capital of the planet, meaning they can control and buy all that they want.
It seems odd that a gunslinger as skilled as Vash wouldn't have any ammunition on him, until you remember he was recently robbed and tied up, and he didn't get much time to sit still between being rescued and the duel. Anything he had readily to hand was probably either expended or taken off him, leaving only whatever he had in his bag — which he didn't bring to the duel.
Roberto points out Vash was not afraid of the MPs, which he wasn't — he didn't fight back even as they beat him, and when the cluster bomb was launched he sighed in annoyance, which is... a strange way to react to inbound missiles. Roberto then adds that Vash was actually scared out of his mind about seeing the red Plant (if you scroll back to check, he's right: Vash's expression is fearful and he's sweating as he stares at it) and asks why. Vash then brings up Knives. Given the last time the two met in episode 9, Knives had killed dozens of humans for forcing their sisters into a Last Run, and sliced off Vash's arm that activated his Gate. It's no wonder red Plants would trigger bad memories for Vash.
- Vash notes that things will "get worse" if nothing is done to help the dying Plant. Now, he could mean that the townsfolk will start to die out, something he is absolutely against. However, Knives is out collecting Plants, which would lead him to target Jeneora Rock for not only their dying Plant, but also their healthy one. In the Japanese this is even clearer: Vash doesn't vaguely say that things will get worse, he says that "something worse will happen".

Episode 2: The Running Man

Vash spends the start of episode two (seemingly overnight at Jeneora Rock) either making more ammunition or just packing some new supplies, hence why he declares he has "extra" bullets the next day.
After divulging some information to Roberto and Meryl, the two reporters start theorizing Knives's motives for stealing the Plants. Roberto ends up coming the closest to the truth, concluding Knives is out for revenge. After watching humans abuse and kill off his kind, Knives's ultimate goal is to annihilate the entire human race to recreate the world as a paradise for him and Vash alone in retaliation.

Episode 3: Bright Light, Shine Through The Darkness

The radio broadcast at the start of the episode that plays over Knives walking to Jeneora Rock warns that there's a sandstorm heading west, it's been intensified by air currents, and that its arrival will likely disrupt Plant operation. Jeneora Rock is on the western portion of the map. A (humanoid) typhoon could be described as an air current. And having a Plant stolen would certainly disrupt its operation. Without the radio operator knowing it, he's not just predicting the weather, but Knives's arrival at Jeneora Rock.
E.G.'s bombs being shaped like viruses make sense, since viruses latch onto their hosts to destroy them. Knives may have thought this was a fitting weapon to eradicate the "parasites" with.
E.G.'s explosive drones having cube-shapes on them doesn't just make them look like bacteriophages. They visually echo the cube that Vash creates (which was also volatile and likely to explode). E.G.'s go from blue to red, but Vash's is purple — in the end, he does not choose a side, fighting to save humans and Plants both.
Most of E.G. the Mines bombs go off on random citizens including Meryl and Roberto. However, even when trying to stop E.G. The Mine from taking the Plant, Vash's bomb is never triggered. Given how E.G. the Mine is working under Knives, he was likely told to not harm Vash, but everyone else was fair game.
- Aside from failure to complete his mission, Knives could have another reason to kill E.G. the Mine. He held Vash at gunpoint, and Knives does not like it when humans threaten harm on Vash when he's around.
- It might be even simpler and pettier: E.G. was standing the doorway. Vash is going to stand there, so E.G. needs to get out of the way. Anyone else would order him to move, but if you've named yourself Millions Knives, there are expectations to fulfil.
Vash freaks out when he hears a piano song being played that the others don't recognize. In a flashback, it shows him and Knives as children playing that song together in a duet. So Vash would recognize the song he and his brother made together. In episode 12 a young Vash claims the song he's humming that sounds like their song calms him down when he's nervous. Knives was likely playing it in hopes of getting a warm welcome from Vash, but unbeknownst to Knives, the song now only instills fear in his younger brother.
The reason Knives brings down his hood in front of Rosa? So she can see how similar he looks to Vash, which will lead to her to become distrustful towards his brother, and blame him for the tragedy that befell her town. Who's to say after stealing Plants from other settlements, this isn't exactly what Knives did to get the people to turn on Vash.
Elendira's appearance and nature imply that her creation was another attempt by Conrad to atone for what happened to Tesla. While Tesla was an Independent Plant torn apart by humans experimenting on her, Elendira was born from human experiments and was designed to be able to survive without relying on Plants, intended to eventually supersede humanity.

Episode 4: Hungry!

Of course episode 4 would be the episode to introduce Wolfwood the undertaker.
Meryl is shown to be the most concerned for the kid the group finds in the gas station, holding onto him as they're swallowed by the sand worm and acting relieved when she finds him after he disappeared. A few episodes later, she expresses guilt over what happened to Tonis, feeling responsible for his injuries because she couldn't hang on to him when Jeneora Rock was collapsing. Knowing this, her previous actions toward Zazie gain new meaning, showing that she was already trying to make up for her past mistake by protecting who she thought was a civilian child.
Vash loves to eat for fun, punishing himself by going without food. Plants, even Independent Plants like Vash and Knives, don't seem to need to ingest anything like food or water at all. While eating serves a practical purpose for him beyond sustenance by concealing his nature, there's something else: his unique ability is forming a black hole that consumes everything around it rather than producing things as a Plant normally does. Vash likes to eat because "eating" is what makes him special.
- Knowing that, Vash refusing to eat at the start of the episode is bookended by Dr. Conrad concluding Vash's Gate is kept closed and locked by Vash's principles/ideals in the episode's closing scenes. Just as Vash won't eat until he decides he deserves to, he won't use the consuming power of his Gate until he's forced to.
A close inspection of Wolfwood's cigarette lighter shows the Eye of Michael insignia engraved on it. Vash has likely seen that symbol before and knows its connection to Knives. Vash knew Wolfwood's true intentions from the start, but decided against interrogating or prodding him for more information.
Wolfwood seems to be barely smoking the cigarettes he has before tossing them onto the ground. Extra materials reveals that a lot of the cigarettes are made from worms. This is likely Wolfwood's way of being spiteful towards Zazie aside from eating the worms since he knows he's being monitored.
Speaking of eating Worms, Meryl never does, mostly because she thinks they're yucky. Wolfwood, ever the big brother, tries to bully her into it because it's funny. Even in the future on a distant planet, brothers try to get their sisters to eat bugs — but Zazie seems also to have taken notice...

Episode 5: Child of Blessing

Monev the Gale's title seems to be more intrinsically tied to the town Vash and the others stumble upon, as if he's the one withholding the wind. When he's revealed to be Rollo, the Child of Blessing who chosen as a human sacrifice to bring back the wind to the dying town, the name is incredibly ironic.
Elendira accompanying the Eye of Michael to collect Rollo for experiments leads Rollo to ask whether she's a sacrifice like him. She laughs and corrects him: she's an "angel". Although she could be playing off of her appearance looking "angelic", Elendira was created from Knives's cells to be a creature neither human nor Plant by Conrad. And the Plants - especially Knives - are referred by the Eye of Michael as "angels".
When Rollo meets Vash, he already seems to know him, but the kid doesn't know Vash beyond the rumors about the Humanoid Typhoon. Vash plays it off by telling Rollo his mother asked to have her son returned home. The photo Meryl later finds of Vash and baby Rollo shows Vash hasn't aged a day since the photo was taken. Like Rosa, Vash was possibly on friendly terms with the townsfolk, especially Rollo's mother.

Episode 6: Once Upon A Time In Hopeland

The English dub gives Wolfwood a very interesting line indeed when Vash asks him why Wolfwood's following him around. "I'm like a cool big brother. You won't smash the bullies' skulls, so it falls to me." Wolfwood is working for Knives to escort Vash safely to July — and not only does Knives consider himself the older brother, that's a simple but accurate description of his reasons for exterminating humankind.
The Bad Lad Gang's gear gets an updated look in this iteration, with axolotls as their motif. Some axolotls are capable of glowing in the dark, and such a flashy fit is perfect for someone like the Bad Lad Gang's boss - Brilliant Dynamites Neon. They're also a form taken by the Aztec god Xolotl, who's the god of fire, monsters... and twins.

Episode 7: Wolfwood

Legato seems to have a vendetta against Wolfwood, who has a strong familial bond with Livio. If Legato is anything like his past incarnations, he might be projecting his distaste for Knives being so obsessed to getting Vash back onto Wolfwood and Livio's "love" for one another.
- Also, the fact that Legato tries to strip Wolfwood of everything he cares about to make him a perfect weapon suggests that Legato might, in fact, be mistaken when he says he doesn't understand his lord's version of "love". He's doing a very good impression of how Knives "loves" Vash.
It seems like there's a huge plothole about how Vash and gang got onto the SEEDS colony ship after Vash collapsed on the sand steamer since that isn't really elaborated upon. Except they mention that the ship is hidden in a perpetual sandstorm. Episode 7 ended with a sandstorm encroaching upon the sand steamer. This implies that Vash either has a tracking device on him or is able to send out some kind of distress signal that allows the SEEDS ship to track him if he needs it.
- Or it was the ion cannon firing into the air. They detected the massive energy burst and realised he was probably responsible, and probably in trouble.

Episode 8: Home

Unlike the manga and 1998 anime, Vash in Stampede was taken in by a surviving SEEDS colony ship very shortly after the Great Fall and raised by them thereafter, which may explain some of the differences in his personality in Stampede beyond him seeming generally more youthful. Vash in the manga and 1998 anime was very quick to distance himself from other people at first opportunity and frequently would go missing for long stretches of time, even from his closest connections. In Stampede Vash still attempts to distance himself from his new companions, but he's a lot less adamant about it and winds up traveling with them anyway. Considering that Stampede's Vash has a more stable support system who he is emotionally close with, it makes sense that he's more receptive to offers of friendship, even when trying to be a loner.
There's a photograph in Vash's room of Luida cutting his hair as a child, implying that the haircut he has now is because of her. If you look at Luida herself, it suddenly makes complete sense that his haircut looks the way it does, because she basically has the same haircut as Vash, just arranged differently - an undercut with messy bangs.
- The way Vash's spiky bangs flop over the right side of his face recalls his old bowl cut, but also resembles Brad's own blond hairstyle. It makes Brad and Luida look more like his parents.
- For further subtle characterisation, when he still had hair Dr. Conrad wore it in a style similar to Knives's hair: an undercut neatly slicked back from his forehead. Knives's hair just sticks up more to look spikier, like Vash's hair is fluffier than Luida's.

Episode 9: Millions Knives

While Vash fosters a community and friendships at Ship Three, Knives likely did the complete opposite. Isolating himself in his piano room, and only speaking with Conrad when necessary. Kinves refuses to make any meaningful connections to the humans who are currently killing his kind with no apparent remorse. Thus, the workers wouldn't know how dangerous Knives truly is, and likely just saw him as a normal kid that Conrad took care of.
July has so much water it's got a canal running through the city, while Jeneora Rock was struggling for lack of clean water, to the point of trying to capture the man who'd been a hero to them for his bounty. The bounty which awards enough money to buy a new Plant. The bounty that was posted by July city, which has a monopoly on water-producing Plants. But of course Knives only is stealing Plants and taking them to July because he wants to save his brethren from the human parasites. Just ask him.

Episode 10: Humanity

Wolfwood nearly falls off his Tomas steed multiple times on their race towards July city. Even though he grew up with baby Tomas chicks, Wolfwood obviously didn't have the chance to spend more time rearing and riding one when he was younger. Hence why he practically has no idea how to keep himself steady, whereas Vash has had nearly 150 years of experience.
Why all the water in the tank below Knives's piano room? Aside from likely being a good place to store the other Plants, July is the water capital of the planet - so Knives has access to all the water he could want for his schemes.
Elendira can create and throw metal nails. But of course. She's partly grown from Knives's cells, and Knives creates metal blades. Her Gate being "weak" might be why she's limited only to nails, as well as why she's more vulnerable to injury than either of the twins.

Episode 11: To a New World

When Vash is first dropped into the water below, he reacts as if he's drowning, attempting to claw his way back to the surface to get air. Then Knives joins him and tells him to calm down, all without any sign of choking or discomfort. Vash was panicking and acting like a human would in that situation, when it's been shown again and again Independents don't need nutrition or apparently air to survive. It further encapsulates the twins diverging personalities, Vash is embracing humanity while Knives is embracing his side as an Independent Plant.
Nai doesn't believe Vash when he tells him Rem promised to never let what happened to Tesla ever happen again to her boys. Viewers who know this part of the manga's story point out how odd it was that Vash seemed so quick in accepting Rem's words and trusting humans. However, you need to remember - this is Knives showing Vash only his memories. Knives is being an Unreliable Narrator, as he wants Vash to see and agree with only his version of events. In the manga, the readers got to see Vash and Rem console and talk through what happened to Tesla and come to an understanding. However, Nai was not present since he was unconscious, which was likely what happened in Stampede, hence the gap in Nai's story since we don't see Vash's point of view.
While Knives could be celebrating their literal birthday (July 21st), he's also celebrating Vash's "rebirth" as a perfect Independent Plant, like himself.
Knives: After all this time, I finally have him back! Happy birthday, Vash.

Episode 12: High Noon At July

A child Nai shows an interest in Western cowboy films whereas Vash voices his distaste for them. This reflects the twins ideals when they get older. Knives finds it acceptable to use violence to protect the people you care about and believes he's the "good guys" taking down the "bad guys". Vash on the other hand becomes the pistol wielder, but would rather avoid any bloodshed at all if possible, as there are other means besides violence for a peaceful solution.
- Alternatively, they both grew into the opposite of what they imagined they would. Vash became the greatest gunslinger history has ever seen, while Nai turned into the bad guy of the story, threatening the people Vash protects.
It says something about Knives that he may have chosen No Man's Land to crash the ships because it was a bit like his favourite cowboy movies — and then when he got it, he found out he didn't like it at all. The "paradise" he longs for bears a deeply suspicious resemblance to the SEEDs ships before the Fall. Knives wanted to grow up, but once he did, all he wanted was to go back to being an innocent child again.
Rem promised the twins she'd protect them. When Vash is running through the field of geraniums to wake up from his nightmare, the Rem-spirit sweeps over him and gives him his coat. Vash's coat is geranium-red — and bulletproof. Even all these years later, so long after her death, she's keeping her promise.
Knives did, in fact, successfully "remake" Vash into a better Independent Plant. It just didn't turn out the way he obviously hoped.
- Though this time Knives didn't force Vash to fire his Angel Arm, his brutality has still left its fingerprints in its construction. Each of the three things used to assemble it (this tri-gun, if you will) – Vash's prosthetic arm, his pistol, and the energy cube – are souvenirs of some kind of trauma that Knives has visited on Vash.
- On the other hand (arm?) there are three factions that Vash aligns himself with - the humans of SEEDS (who gave him his arm), the humans scratching out a living on the surface of No Man's Land (one of whom Knives took the pistol from) and the Plants (whose power Vash used to create the cube). The Angel Arm, like his changed coat and glasses, represents Vash's identity as a unifier of all three that he's finally openly declaring. Even more so when you realize his Angel Arm has a similar shape to the SEED ships - the symbol of humanity.
- Also, Knives used his abilities to make a cloak shaped like a chrysalis, while Vash uses his to build a weapon shaped like a spider. Huh.
In the manga, the appearance of Vash's Angel Arm resulted in a crater being blown in the fifth moon. In Stampede, certain shots frame Knives as backlit by the moon, foreshadowing his death via Angel Arm.
- Speaking of foreshadowing, the twins' first proper confrontation takes place in what would become the city of July. Vash points a gun Knives gave him at his brother. All those years later, again in the city of July, Vash pulls the trigger and Nai "dies".
Rem is associated with red geraniums; her role as Vash's connection to humanity results in a Color Motif where red symbolizes humanity. On the other hands, Plants are blue. Vash's coat reflects this: the red faces outwards, reflecting his desire to fit in and be a part of humanity, while the inner lining is blue/teal, reflecting his desire to hide his inhuman nature. This further extends to red Plants, which are ill and malfunctioning, reflecting Vash's belief that he is innately broken or monstrous. During the climactic battle against Knives, his color scheme changes to purple, symbolizing a union of humans (red) and Plants (blue).
- This symbolism also extends to Knives, who is predominantly associated with blue and believes himself to be the champion of his brethren, the Plants. When he's burning up in Vash's Angel Arm, his extremities turn red, symbolizing his inability to overcome humanity and Vash's unity. Alternatively, Knives is more human at his core than he'll ever admit to being even at the moment of his death.
Vash's wing appears to not be fully formed compared to his brother's metal wing. Since this is Vash's first time fully embracing and using his powers, it's likely not had time to make a proper construct of itself like Knives.
Meryl's new outfit, as well as demonstrating her more jaded outlook, draws from each of her companions who are now lost to her in one way or another. She wears brown slacks like Roberto's suit jacket, sunglasses like Wolfwood, and her earrings have hoops like the one Vash wears.

Fridge Horror:

Episode 1: Noman's Land

Vash being tied up and hanging amongst those other corpses in the first episode. It's unclear whether Vash was tied up with them, they were there before he was, or how long they've all been there. After all, since Vash is a Plant, he can't starve or die from dehydration as humans very much can.
One of the people Meryl passes by while entering town is a man lugging a coffin on his cart. Rosa later tells the group how their water Plant is broken, and they have to get water from the next town over - likely days away. How many people have started to die out due to lack of clean water?
The bird vulture creatures that were pecking at Vash's "corpse" and hanging around Jeneora Rock fly off and head towards July. Zazie is later shown to also be able to control not only the bugs, but the Grand Worm and these buzzards as well. Meaning wherever these creatures are, Zazie can spy on anyone and immediately report back to Knives.
Vash informs Rosa that the town's Plant in the red container was dying, and they needed to get it replaced soon or their situation will just get worse. Vash is covered in red like the dying Plant whereas Knives is associated with blue and white, the healthier Plant. After July, Vash's hair darkens, showing that he's slowly dying due to the massive amount of energy he expels. And he has no way of getting that energy back.

Episode 2: Running Man

In the opening scene as Vash is restocking on bullets, you can see E.G. the Mine's machines scuttling around in the back, with Vash none the wiser. How fast did Knives send E.G. over to Jeneora Rock and where had he been hiding for that entire time since? Given how fast Zazie relayed Vash's location in the previous episode, probably not too long.

Episode 3: Bright Light, Shine Through the Darkness

Knives has a habit of cutting off the arms of the people he comes across. In episode 9 it reveals he was the one who cut off Vash's arm when his gate summoned a black hole and Knives cut it off before it could possibly kill Vash. Does he do that knowing Vash is around Jeneora Rock to possibly stumble across this scene and is mocking him? Or even taunting Vash for choosing to side with humanity which is what lost him his arm in the first place?
- Another reason is that because Vash lost that arm due to his love for humanity, Knives retaliates to the other humans he meets by taking their arms as a sort of revenge for Vash.

Episode 5: Child of Blessing

At first, Rollo calls out to his mother with his original voice, but Monev was likely modifying his voice with his mask in an attempt to not frighten her. He likely hoped his mother would still love him and wanted to return home. When she got scared instead, that pushed him over the edge and caused Monev to destroy the town.
Rollo's village ran without a Plant (or at least tried to), but that didn't stop the Eye of Michael taking their children as sacrifices. Knives calls humans nothing but parasites, but his own cult takes from humans who've never harmed a Plant in their lives.

Episode 6: Once Upon a Time in Hopeland

Wolfwood sees himself as a monster, the Punisher of the Eye of Michael. In episode 5 he kills Monev the Gale out of mercy and belief he was a monster that couldn't be saved. Rollo was called a "child of blessing" when he was experimented on, and so was Wolfwood - another child of blessing. He likely sees a lot of himself in Monev and truly believes he will never deserve mercy or redemption.
Livio moves around like he's a puppet or under some heavy drug usage when he fights Wolfwood and Vash. Given how much of a wild card Razlo is when he's in charge, the Eye of Michael likely use whatever they have to keep Livio as semi-conscious as possible while still having Razlo locked away. The eye piece he wears over his left eye may be for more than just aesthetic choices, since Livio comes back to consciousness when Wolfwood destroys it.