Episode 28.5, "The Last Episode Ever". It first aired on April Fools Day.
Episode 45.9, "The Greatest Episode EVER". An episode made entirely with paper cutouts by Gus Sorola while the rest of Rooster Teeth was out of town.
Out of Mind: Part 2's flashback segment comes off as this retroactively, seeing how it shows Texas and Alpha-Church talking casually while it's shown the Blues and the Project were capable of actively interacting with one another. It's later shown that this whole flashback was very incorrect in many ways, and it's never remotely explained why Texas' memory would be so wrong.
Ensemble Dark Horse: Viewers of Out of Mind loved Delta and York. And both Sister and Junior were very popular despite only having starring roles in Season 5.
Franchise Original Sin: In the beginning, the show was always about laughs and invoking the Rule of Funny. Antics like a robot head that could built other robots, time travel, ghosts and being transported into what was all but stated to be an actual game of Halo were commonplace and accepted due to the quality of the jokes. And even when the series moved into more serious fare, the show was good about retconning or sidelining those as needed while doling it out just right to ease the tension. It only truly became more of an issue in Season 16, which went whole hog on being funny by suddenly introducing gods, real time travel and a cyclops done in live-action. Such a sudden veer back into territory even more outrageous than the first seasons had done wound up coming across as too jarring and unexpected.
Growing the Beard: It was during Season 3 that the series slowly began to head towards a plot-driven structure with some moments of genuine Character Development. This was dialed down a bit in the fourth season, but soon returned in the middle and would stay that way for the rest of the arc's run.
After learning of Private Jimmy'strue fate in Season 14, Tucker and Church's conversation about him in "A Shadow of His Former Self" is subtly horrifying.
Sarge's hilarious Blood Knight tendencies, Insane Troll Logic, and habit of shooting/trying to kill poor Grif are all rather uncomfortable to watch as not only would Season 14 display him as being so crazy that he killed his own C.O. when being picked out as the Blood Gulch Red Team's sergeant since he thought he was a Blue in disguise, but later seasons (most notably Revelation, Season 15, and Singularity) would start to take a more critical and tragic view on how much of a negative impact being in the military for so long has had on Sarge's psyche.
Captain Butch Flowers dying of an allergic reaction to some medication is this twofold; the first reason is that we find out this was almost certainly Gamma torturing Church For the Evulz in Season 10, and the second is due to Monty Oum's tragic death from a severe allergic reaction after surgery in 2015.
Most things about Captain Flowers become this in hindsight after Seasons 10 and 14 reveal that he's actually Freelancer Agent Florida, a ruthless sociopath who barely batted an eyelash as Sarge killed his subordinate Lemons (even cheerily thanking him for finding the perfect candidate as Lemons pleads for help over the comm), and forcefully implanted the Alpha A.I. into Private Jimmy, completely shattering the image of A Father to His Men he had up until then.
Tex not showing any hesitation to kill Grif when asked to, once Season 15 reveals that it wouldn't be the first time she horrifically killed a simulation trooper in orange armor with no remorse (though her using Omega at the time then admittedly complicates the situation).
While threatening Andy, Tex emphasizes how he will be just a memory after she detonates him. The amount of irony is staggeringseeing what becomes of Tex after both Reconstruction and Revelation.
Caboose's cheerful shout of "Connecticut!" is this when Tex and Wyoming meet each other again, now that the audience knows that Connie was one of the few Freelancers Tex had any kind of emotional bond over. Furthermore, Connie's death had the greatest impact on her out of anyone and helped kick-start her Heel–Face Turn.
Most of the second half of Season 4 and all of Season 5 portrays Church as on the verge of reaching his Rage Breaking Point as he struggles to keep Blue Team at least partly functional despite the world seeming to fall apart around them. This is largely Played ForBlack Comedy at the time, but The Project Freelancer Saga would later reveal that the Alpha A.I. was successfully tortured past the brink of insanity multiple times by having him be Forced to Watch as the people he cared about most died horribly and he was told that it was all his fault. So in essence, Church is pretty much going through his worst possible nightmare all over again throughout the last portion of The Blood Gulch Chronicles... and he doesn't even realize it.
When Grif's Sister appears in Season 5, her having run away from home to be with him in the military is Played for Laughs and Hand Waved away at the time as the result of her being The Ditz. Not only would later seasons take a more serious look back at the Grif family (with Season 13 claiming that Grif was The Unfavorite and he was Promoted to Parent due to the siblings' parents being utterly despicable), but that (as revealed in Singularity) Sister actually ran away from home out of guilt for accidentally burning down her and Grif's childhood home.
While Omega's absurd plan to conquer the universe with Wyoming and Gamma's help on the surface can at least be laughed off as the result of the two's manipulations on their own, later seasons would imply that they were still working for Freelancer Command all along (with Tex/Allison instead being the Rogue Agent) and this was actually Project Freelancer's best plan to stop the Great War.
Church discussing battle tactics and strategy with Captain Flowers during the Season 3 flashbacks is a lot sadder after Season 9 would show that the Alpha was used to help plan out the Sarcophagus heist that would ultimately result in its horrific Cold-Blooded Torture. In essence, the Alpha overlooking battle plans is the exact thing that got him stuck in Blood Gulch in the first place.
During Season 3 and when Church is traveling through time, he meets up with his past self from Season 1 when he's going through his first death, with Future!Church awkwardly telling his past self that "You should rest now." This is really hard to watch now after Epsilon-Church Mercy Kills Tex in Season 9 after she makes it clear that she's tired of being brought Back from the Dead only to end up as a Cosmic Plaything and by this point just... well, "wants to rest."
The time loop shenanigans in the aforementioned season also have Church giving a heartfelt apology to Tex for failing to be a better person to her than he should have been, which is pretty depressing to see after later seasons show how messed up their romance really is and how this can be seen as the Alpha subconsciously trying to apologize to Beta for him having doomed her to always fail at the last second.
Hell, pretty much all of Church and Tex's Slap-Slap-Kiss dynamic becomes this once later seasons show how they're actually both Loving a Shadow, as their entire relationship is only a reflection of the Director and Allison Church's romance.
In "Biting the Hand", Tex briefly recounts the events of the Out of Mind miniseries to Church, with the latter asking if Carolina was with York when she met up with the latter. While it's just a minor detail at the time, it's rather sad to see after The Project Freelancer Saga would reveal that Church can't remember almost anything from his time as the Alpha A.I.. That means one of the only things he still remembered from that period was the daughter of the man he's based on.
Tex gently whispering "Goodbye" to Church as she lifts off on the Pelican in "Why Were We Here?" is pretty tragic to watch after The Project Freelancer Saga would delve into how the Director (and, to a lesser extent, Carolina) never truly got over the death of Allison Church because they Never Got to Say Goodbye.
In Season 1, Grif saves Sarge from a bullet wound to the head with CPR, and Sarge (unfairly) chews him out for such a stupid choice of medical attention. Years later, when mass shootings became a major hot button issue in 2018, Rick Santorum got into hot water for suggesting students learn CPR.
In the Season 2 DVD commentary, Burnie Burns noted during the "dongle flip" scene that they promised themselves never to do teabagging... only to use the crouch motion in that suggestive way. During the next season there is actual teabagging, and it's exactly to mock the sort of player who does that (something the DVD commentary even makes sure to lampshade).
A panicked Grif begging Tex to not hit him in the face once he insults her is much funnier to watch after later seasons have all iterations of Tex focus almost solely on giving Groin Attacks to the poor guy. Be Careful What You Wish For, Grif!
Caboose claiming that Church is a "gay robot" after learning of Tex and Church's relationship in Season 1 is absolutely hysterical after Season 14's "Get Bent" would reveal that Epsilon-Church was perfectly fine being with a male version of Tex while stuck in the Memory Unit.
One of Church's awkward attempts at a Pre-Mortem One-Liner in Season 2's "An Audience of Dumb" becomes this after The Reveal at the end of Reconstruction, considering that this scene has him partnered up with Tex to take down O'Malley.
Also, Church's exasperated cry of "Holy crap, who is running this army?!" in Season 1 becomes utterly hilarious after the audience finds out in the season finale of Reconstruction that Leonard Church is the person actually running the Red and Blue Armies!
When performing a hostage exchange near the end of Season 2, Caboose calls Donut "Major Cinnamon Bun." Keep in mind that Season 2 of Red vs. Blue aired three years before the first Adventure Time short even aired.
Caboose's statement of how "time is made of circles" is pretty hilariously prescient after Singularity would reveal that black holes in the RvB universe loop backward in time to before the Big Bang.
In Season 4 when the Blues are hunting for the Alien, Tex sarcastically wonders aloud that if she kills Church while he's a ghost than if that means he would "come back as a ghost of a ghost." That's essentially what happens in The Recollection: Church is killed in the finale of Reconstruction, and is revived in Recreation via Epsilon and Caboose's memories of him.
Sheila's appreciation for her new Pelican-class dropship body is quite amusing when it turns out she's almost certainly based off of the Freelancer Dumb A.I. F.I.L.S.S.
"No, another ship, then that ship left and this ship crashed in the exact same spot. " Come Season 17, and the revisiting of this moment has something very reminiscent of this sarcastic answer: Sister's Pelican doesn't land on Donut, only for another one to appear and crush him.
In the first alternate ending for Episode 100, all of the Reds and Blues end up in a massive free-for-all that ultimately ends with a Total Party Kill, with Caboose being the last character left alive (at least until a vehicle falls on him). Many years later in 2020, DEATH BATTLE! made an episode showing which team would have won if every character had fought seriously like in Episode 100's alternate ending... and it also ended with Caboose as the last one alive, except this time he survives the whole thing.
Magnificent Bastard: Agent Wyoming, real name Reginald, and his AI partner Gamma, representing the Alpha's deceit, are the primary operators of Omega's plan. Hired by Omega to assassinate Tucker, Wyoming allowed a bomb to go off that knocked the Reds and Blues unconscious. Gamma manipulated an alien race into a believing prophecy, leading one alien to impregnate Tucker before being killed by Wyoming. After Wyoming sent Omega back to Blood Gulch to find a new host, he confronted and killed Agent York, and managed to escape Texas. Wyoming and Gamma reunited and headed to Blood Gulch to retrieve Tucker's alien son for Omega to possess and control the Covenant. Wyoming used his time distortion unit to cheat in battle, and when seemingly killed unleashed time copies to continue to fight. Wyoming's final push before his death was to reveal the full extent of his plan to get Tex on his side.
Never Live It Down: Caboose really only killed Church once with a tank (and that wasn't even entirely his fault). He sort of killed Church while the latter was possessing Sarge, but as a ghost form, he couldn't be killed, and Sarge got better. Yet they won't stop giving Caboose crap about killing his own men. Though granted, this may be because this won't be the last time that this happens.
One-Scene Wonder: Private Jimmy, who only appears in Church's flashback in Episode 10 and is used for a hilarious Death as Comedy joke. He was even brought back for the Season 14 Origins Episodes, though his reappearance goes through a significant Cerebus Retcon.
Rescued from the Scrappy Heap: Downplayed with Caboose. When he started out, he was just a slightly slow Deadpan Snarker with a rather flat affect that didn't make him very memorable. However, after the writers Flanderized him into becoming a CloudcuckoolanderDitz, he became easily the most popular character out of the entire series.
Doc: Everyone! I have something to say! Tucker and I are in love, and we're leaving! Tucker: That's right! We're getting married and there's not a damn thing you can do about it! Not even you, French-Speaking Lopez! Lopez: [Mister Tucker, you promised your love to me!]
The Scrappy: Not many fans like Andy the Bomb, since he had no character traits or depth outside of being a massive (not to mention unfunny) Jerkass. It's pretty telling that he hasn't made any appearances in recent seasons outside of recordings and has been mostly forgotten.
Seasonal Rot: While Season 3 had received some praise for its more plot driven structure, it was also criticized for downplaying the sharp dialogue and character interplay that made the first two seasons so enjoyable. When Season 4 returned to the show's original formula, many fans were pleased.
Stoic Woobie: Later seasons reveal that Tex had been one of these the whole time. She knew exactly the kind of torture that Church had been through, and was simply trying to watch over and protect the broken remnants of someone she had loved (to the point where she had demolished an entire military base/spaceship trying to save him).
Overlaps with Jerkass Woobie to an extent when you realize the reason why she acts like such a Jerkass to Church: Every time she sees him, she's reminded of her failure and that the Alpha will never be what it once was. No wonder she can barely stand to be around him, especially after the Alpha Took a Level in Jerkass following the attempted breakout. Could also be a façade since she likely acted so cold to him in order to keep him distant or from becoming too attached to her, since it could — and did — lead to him discovering what he really was.
They Wasted a Perfectly Good Character: Grif's Sister (whose first name, Kaikaina, isn't even mentioned in the show itself until Season 15) has barely any effect on the story, and disappears almost entirely after Season 5, despite all the fun gags or plot complications that could be built off Grif having a sibling on the other side.
Values Resonance: In a weird sense. There's something rather remarkable about The Blood Gulch Chronicles giving such a dim view on militarization and war for an American web series that only started to air less than two years after The War on Terror started.
The show is actually remarkably popular with American veterans for its depictions of the frustratingly inane and bureaucratic aspects of the military.
The Woobie: Both Donut and Caboose. Sure, they both might be as dumb as posts, but they're both still just so adorable and sweet, which makes it all the sadder when things go horribly wrong for them.
Based on a True Story.