"Prisoner of War" and "Assault on 42" both see Captain America leading heroes and villains trapped in an intergalactic prison in fending off a destructive alien force together. Worse, Disney XD aired the latter episode only a little over a month after the former's premiere. At least the motive behind fending off the alien differs in each of those two cases.
"Ultron Unlimited" seems almost like "Gamma World" meets "Infiltration", as it has a villain who wants to remake the world in his imagenote The Leader turns people into monsters in "Gamma World," Ultron replaces people with robots in "Ultron Unlimited", and evil duplicates of the Avengers assisting a world domination plannote Skrull Avengers in "Infiltration," robot Avengers in "Ultron Unlimited". However, you could argue that this episode takes those plot points into different directions.
"Some Assembly Required" and "The Deadliest Man Alive" both have a villain manipulating the Hulk into acting even more destructive than usual, nearly destroying his relationship with the other Avengers in the process. They even both end with Hulk quitting the Avengers, although the second time at least has Hulk assure the others that he'll return eventually.
Redemption Demotion: Vision as a villain- Able to take on multiple avengers at once, easily trouncing them, phasing away from or getting too dense for every attack. Vision as a hero- Frequently surprised and knocked down, despite clearly still demonstrating the abilities.
Red Eyes, Take Warning: Wonder Man, and Ultron after he goes rogue. He even makes it his trademark by making every computer screen in the world that he hacks, glow red.
Redshirt Army: The army of Ultrons used as reinforcemen during Kang's invasion. They were very lucky that one Ultron survived, to hack Kang's ship.
Reed Richards Is Useless: As of the finale, despite the myriad of amazing technology and dimension hopping, mankind has still explicitly made it further in outer space than real life humanity has (the moon).
Retool: Jeph Loeb oversaw one starting in episode 41, with help from Man of Action Studios, deciding that people would prefer standalone episodes to arc-based. Loeb cited the desire for people to not have to pick up the show midway through and say "I don't know what's going on." He also brought out a mandate that stated episodes should be focused on the 'core' Avengers, meaning Iron Man, Captain America and Thor, with less focus on the rest of the team.
Rock Beats Laser: Subverted by Wakanda. While they cling to archaic values and government, those spears they chase people around with are made from tech more advanced than the Iron Man armor!
Kang's forcefields casually shrug off Iron Man's strongest blasts, but Hulk just as casually breaks right through them with brute strength.
Only the first time. After that, the Hulk never gets another hit in, though he makes up for it by subverting it with Rock Distracts Laser:
The Hulk throws a couple of boulders at Kang, who effortlessly destroys them
Kang: You seek to defeat me by throwing rocks at me, you mindless monster?
Hulk: It's called a distraction, smart guy.
The Black Panther hits Kang from behind with his vibranium daggers, causing the first real damage to Kang in the fight.
Rogues Gallery: And not just the Avengers villains. We also get villains for each individual member.
Sadly Mythtaken: Just keep in mind that they're going for comic book accuracy with Thor, not mythological accuracy.
Sanity Slippage: General Ross shows signs of this is his first appearances. He's not fully gone, but his obsession with the Hulk is clearly starting to get the better of him. Meanwhile, Graviton takes a flying leap off of the slippery slope and never looks back.
Iron Man: Pepper, guess who I ticked off this morning? I'll give you a hint: his name rhymes with "Boom"
Captain America plays this straight with Bucky's name when Bucky sacrifices himself to save Cap from perishing in an explosion. It also becomes the very first thing Cap says after awakening in the 21st century.
Science Is Bad: Thor holds this view (and he can be forgiven considering some scientific monstrosities such as the massively deformed head known as MODOC), though the show as a whole avoids it as it has a scientist and a Techno Wizard as some of the heroes (Pym and Stark, and you can add Banner on the rare occasions he's not the Hulk). When facing one set of monsters, Giant-Man refutes Thor's view and states that science didn't make the monsters, people did using science very irresponsibly. Iron Man is also quick to gloat to Thor when magic turns out to be Not So Different and is abused just as easily; after which Thor opens up a little to the idea of technology being helpful.
Scifi Writers Have No Sense Of Scale: During the Skrull invasion, the Skrulls begin to attack with hacked satellites. So, Thor goes to the sky and destroys them all. The problem is that there are satellites all around the globe, and the visuals make it seem as if they were all a few blocks of distance of each other
Sexy Walk: Black Widow and Maria Hill both get on this.
Shoot the Hostage: Hank resolves a hostage situation in "To Steal An Ant-Man" by shooting the hostage with a "Pym particle gun", harmlessly shrinking her.
Shooting Superman: Wasp's stingers rarely do much. Lampshaded in "Come the Conqueror": "Man, I gotta find bigger stingers!" - before trading up for the Quinjet.
One of the photos Wasp took in the tie-in comic "Team" has a caption reading, "Wow. Just...wow. 'Nuff said."
Another shout out involves something from behind the scenes, many fans felt Marvel was a sell out but its to similar to an episode that introduces Wonder Man (purple guy, made of ionic energy) who had a failing business, as Iron Man stated "..I didn't buy him out to finish him, I bought his company to save it." - Many many fans feel this was a hint.
After Captain Americanote rather, the Skrull disguising as Captain America asks Johnny Storm which member of the Fantastic Four he is, Johnny exclaims, "How could you not remember?" In context, Johnny probably feels frustrated that Cap would forget the time he saved him, but viewers could also interpret this as a reference to Chris Evans playing both characters in live-action movies.
The second season premiere even references the story where Doom shot the Baxter Building into space.
The episode "Along Came a Spider" features an abridged quote from The Amazing Spider-Man #537. This is followed up with Spider-Man asking if he can be Cap's sidekick rather than his snarky/admiring response from the comic.
The Avenger's Mansion's doorbell is the NBC chimes.
Silent Antagonist: Skurge the Executioner has no voice actor. He never even makes grunts or battle noises.
Squash Match: Each series of shorts first pits the hero against a weak, easily dispatched villain—Iron Man against HYDRA grunts, Hulk against Absorbing Man, Thor against the Wrecking Crew—to show off his powers before moving on to a larger, more challenging threat.
Snake People: The Serpent Society is a group of snake-themed supervillains; although most of their snake-like appearance and abilities come from cybernetic limbs and such.
SpaceX: Iron Man summarized the Guardians of the Galaxy as "Space Avengers."
Superhero Paradox: Briefly addressed in the Ultron imparative, but mostly subverted so far. While Ultron's mayhem was eventually caused by their activity, and Wonderman wasn't created until the Avengers were formed, most of the villains were already established criminals during the breakout and Loki's plot to release them all was already in motion when the heroes began showing up.
Take That: Black Panther's origin is a Take That to Reginald Hudlin's run on the character's comic book. According to Wakanda's traditions, all someone had to do to become the ruler of Wakanda was win a wrestling fight, exactly as it was in Hudlin's Retcon. As Man-Ape took advantage of this (cheating when he fought T'Challa's father) and became a cruel ruler and sold vibranium to villains, T'Challa points out how stupid this "tradition" was. After he defeats Man-Ape and becomes the new and benevolent Wakandan king, he abolished this tradition.
Continued in Behold the Vision when it's revealed that even though he finds this law stupid, he never actually abolished it, so Hawkeye attempts several time throughout the episode to use this oversight to take over Wakanda to get back at T'Challa for leaving the team. it doesn't go in Hawkeye's favor.
Possibly one to its sister show Ultimate Spider-Man: "I told you never to call me Power Man, Danny."
However, when Cage got a solo series again for the first time afterPower Man And Iron Fist ended, he went back to just being Luke Cage, and really did correct everyone who tried to call him by his old name. Ultimate Spider-Man is the odd one out for bring the name back for the first time in decades.
After saving a trapped man in a truck Spider-Man tries to sound impressive by saying "I'm Spider-Man" in a gruff voice, causing the man to ask "What's wrong with your voice?". This is probably a reference to Christian Bale's Batman voice and the (in)famous "I'm Batman" line.
Skrull Captain America can be seen as a dig towards the Ultimate version of him, considering he takes on the costume and many of the personality traits of the Ultimate version.
Tap on the Head: Hilariously defied. In a flashback to World War II, a mook clubs a distracted Captain America on the head with the butt of his rifle, clearly meaning to knock him out... but Cap just looks annoyed, and the mook takes a nosedive off the bridge seconds later.
Team Hand Stack: When Captain America, Hulk, the Wasp and Hawkeye agreed to stay being Avengers, after all the others left.
Team Spirit: If episodes like "Breakout," "Widow's Sting," and "The Casket of Ancient Winters" don't give you a stronger understanding of the power of teamwork, you must not have paid much attention.
Teeth-Clenched Teamwork: Thor and Hulk have a bit of trouble getting along at first. May be because they're more than a bit similar.
Technical Pacifist: Ant Man will try ever other option available before resorting to violence, but when he pushes that button on his belt, you better hope you aren't in his way.
Tempting Fate: When Strucker and Grim Reaper are about to escape, Grim Reaper temps fate by saying "That was easy". Cue Nick Fury landing on the hood of their flying car.
When Agent Woo wants to talk to Tony about The Vault's security:
Iron Man: Whatever it is, I'm sure it can wait a day.
Graviton, while fighting the Avengers sans the Hulk, actually thinks it's a good idea to steal Hulk's catchphrase. May be justified in that he spent the last 10 years in induced coma, he may not even know about Hulk's existence at all before the fight.
Leader: "With the Avengers defeated, who can stop me?" (Cue Hulk and Hawkeye crashing in)
In SWORD Gyrich was complaining that the US was spending millions of the project, and so far they had never even saw an alien... then, a Kree ship appears.
Lampshaded in Emperor Stark. Vision, Hawkeye and Ms Marvel take out some iron man robots guarding the Quin jet.
Vision: That was of minimal difficulty.
Hawkeye: Did you just say it was easy? You never say it's easy.
Becomes a Brick Joke in "Live Kree or Die", when Vision reminds Hawkeye of his own words of wisdom after Clint claims that defeating one alien monster was easy. Cue dozens of monsters rising up from the ground.
10-Minute Retirement: Subverted in "Some Assembly Required". Even after coming back to save the team after shaking off Enchantress's manipulations, it appears that Hulk still has some issues to work out with the main team.
Double Subverted. Hulk eventually did return, on the condition that Hawkeye stays too.
Subverted Again Post season 1 when Hank Pym leaves the team and remains off the team long after he finally makes an appearance in season 2. He even goes so far as to completely give up his Ant-Man equipment to Scott Lang.
The Reveal: Mockingbird got replaced by a Skrull..
Thematic Theme Tune: "Fight as One", which opens every episode from the first season, describes heroes' personal struggles without referring to anyone by name. Only a fleeting use of the phrase, "Avengers, assemble!", tips this off as a song about the Avengers.
Theme Tune Extended: A version which describes all of the first season's Avengers, instead of just four, never got released. The singers might not even have recorded it. However, the deleted lyrics have become available to read.
There Is No Kill Like Overkill: Iron Man's reaction to getting overwhelmed at the Vault breakout. He hacks the security system and blows the entire place sky high.
There Was a Door: Given the choice, Hulk busts through the ceiling in lieu of taking the stairs.
Lampshaded by Iron Man when his conversation with Thor is interrupted by Hulk kicking down the door to deliver the villains that he and Black Panther had captured.
Iron Man: You know you didn't have to do that, the doors open automatically.
Throw It In: The storyboard artist of "The Private War of Doctor Doom" drew the Thing holding potato chips instead of poker chips, so the writers added a line where Johnny tells him, "I think they meant poker chips."
Time Travel: Kang the Conqueror, the Master of Time, is from the 41st century. He tries to Set Right What Once Was Wrong (in his own eyes) by traveling back in time to destroy Captain America. His story arc includes a Temporal Paradox with the Avengers trying to prevent the Kree-Skrull war from laying waste to the entire planet, but to do so, (according to Kang), Captain America must die.
The newsreel reporting on the apparent death of Captain America refers to him as, "Earth's mightiest hero."
Captain America's speech for all the heroes who came Back for the Finale to help fight Galactus begins by calling everyone, "Earth's mightiest heroes."
Title Sequence Replacement: When episodes 20-26 aired overseas, they contained the same opening seen in preceding episodes. When Disney XD aired these episodes, they began with recaps of previous events, and also contained a new, shorter intro. Later, these episodes became available for legal download at iTunes, streaming at Netflix and Marvel's website, and DVD, boasting no recaps, and the same opening from preceding episodes.
Black Panther: This is not the path I laid out! We should avoid this area! The jungle here is too well protected!
Iron Man: Don't worry, the Quinjet has the best cloaking technology there is. Mine. (cue laser attacks)
Black Panther: Wakanda's defense tech is better.
Too Dumb to Live: Really, Absorbing Man? He puts a dent in your metal body, and you decide that turning to rock will be the best way to fight The Hulk? But then again was dumb enough to pick a fight with The Hulk to begin with, so honestly it isn't surprising that Absorbing Man made such a glaring tactical error.
Took a Level in Badass: Pym is a Technical Pacifist for awhile, but after the incident with Ultron, he became more and more violence-prone, mostly when Jan was in trouble. For example, in "The Fall of Asgard", when Hank and the unconscious Jan are attacked by Frost Giant's in another realm, he goes ballistic to protect her, grabbing a Giant's ax and annihilating three of them (off screen).
Tron Lines: Tony's bodysuit he wears under the Iron Man armor looks like some of the suits worn in Tron: Legacy.
Likewise the design on Hank's suit will glow when he activates his powers.
True Companions: The Avengers initially begin as a group of strangers with a lot of problems, rubbing each other the wrong way, getting into fights, etc. Over time the team eventually become good friends, right up until the Skrulls come in and start sowing distrust amongst the members, leading several members to quit. However, once again they pull together and begin to get over their difficulties, culminating in the third to last episode of Season 2 where Hawkeye plans to save the Earth by traveling into a wormhole and destroy the device inside it that's tearing apart Earth's sun. Captain Marvel explains that doing so would leave Hawkeye in Kree space, stranded in a hostile territory and completely alone. The words are barely out of Mar-Vell's mouth when Thor speaks up.
Thor: "Nay! Not alone. I will accompany him."
Ms. Marvel: "Me too."
Vision: "As will I."
Iron Man: "Sounds like we've got a plan."
Every single Avenger present chooses to accompany Hawkeye through the wormhole, knowing it might be a one way trip, rather than let him face it alone. The group that Hank Pym once called a group of strangers has finally become a team and family.
Tuck and Cover: Two episodes in a row ("Living Legend" and "Everything is Wonderful") Jan has been shielded by another Avenger from an explosive blast. Which works because she's tiny.
Captain Marvel does this to shield Carol and somehow ends up transferring part of his powers to her.
Unusually Uninteresting Sight: When Nick Fury is attacked by Strucker, he has a few years drained from him which turns some of his hair grey. No one seems to comment on this change but since SHIELD faces a multitude of odd threats daily, it could double as Fridge Brilliance, considering it's probably the least odd thing that has happened to one of their operatives. That and that he got off easy compared to the other SHIELD agent that had the same thing happen.
The Vamp: More of less implied to be the case with Vapor, who invades Captain America's Gamma protection suit to kiss him.
The Enchantress, at least for Thor. Not that it does her any good.
Video Wills: Iron Man made one for the New Avengers, basically telling them, "The Avengers and I are dead, so now it's All Up To You." It also grants them ownership of Avengers Mansion and all the equipment within.
Viewers Are Goldfish: Season 2 got pretty bad at this. The redone opening is way more expository, the previews go out of their way to remind viewers of the simplest facts from previous episodes and the first ten minutes are a recap of the team to the person who most wouldn't need it.
Villain Episode: None of the full episodes are like this, but two of the micro-episodes, "The Isle of Silence" and "Lo, There Shall Come a Conqueror", focus on Loki and Kang, respectively.
Exploited the first time he ever tries to escape, Cap and Bucky follow him. It turns out he was planning, or at least ready, for this, as he escapes his escape pod in a ejector seat, leaving Cap and Bucky to die.
Enchantress and The Executioner pull it off too. They used a portal to get out though.
Also pulled off by MODOC by revealing that the AIM base also works as an escape ship.
Virtual Reality Interrogation: In the second season, after a prolonged period of torturing (off-screen) for information without success, Captain America's Skrull captors have his next interrogation "interrupted" by a rescue by the other Avengers (actually shapeshifted Skrull). It doesn't work though, as Captain America sees through it immediately.