The 2006/2007 Marvel Crisis Crossover.The New Warriors, during the filming of a Reality TV program, unthinkingly start a fight with several fugitive supervillains (including Nitro) in the middle of a suburban housing development in Stanford, Connecticut. Demonstrating power well in excess of any he's ever shown before (due to secret drug treatments provided by a Corrupt Corporate Executive), Nitro quite literally explodes - killing all of the New Warriors (except Speedball) and 612 civilians, including the entire population of an elementary school.This sparks a flurry of anti-super feelings in civilians. In the wake of House of M (the previous Crisis Crossover) and Secret War, Congress decides they have to act to control all metahumans, and the Superhuman Registration Act (SHRA) is passed. Although different individual comics in the crossover treated the act in slightly different (and occasionally inconsistent) fashions, the most commonly used presentation of the SHRA included these features:
Mandatory registration of all superpowered individuals (whether active as superheroes or not)
Mandatory registration of all costumed crimefighters (whether superpowered or not)
All crime-fighting and lifesaving activity by non-registered superheroes is illegal
All registered heroes are to attend - and pass - mandatory government training (waivers were issued by Tony Stark for himself and his pro-registration Avengers comrades)
All registered heroes are potentially liable to be called up into active government service, at the discretion of the government, without the option of refusing
Captain America refuses to register and hunt renegade heroes, then forms the Secret Avengers, an underground organization that resists the Act. The X-Men declare the whole mess someone else's problem (Although they do point out that following House of M, there simply isn't enough mutants in the world to get involved), and Tony "Iron Man" Stark leads a SHIELD force to help capture all renegade metahumans, hero or villain. The US government, with Stark's concurrence, also puts together a task force of supervillains - the New Thunderbolts - for the purpose of hunting down unregistered metahumans. Some of the most psychopathic and violent villains imaginable (including notables like Bullseye and Venom) are, against all sense, released back onto the streets for the government-sanctioned hunting down of and crippling of unregistered heroes. (Also against all sense, the government hires Deadpool for similar duties.)The crossover was similar to, but far more extreme than, previous Super Registration Act plots in comics. It is also notable for big changes in the status quo, including the death of Captain America and the unmasking of Spider-Man (among several other heroes). Despite Joe Quesada (then-editor-in-chief of Marvel) promising that Spidey's unmasking would not be undone via a "magic retcon" (those being his exact words), Spidey's unmasking was retconned as a part of Quesada's wildly unpopular pet storyline One More Day - by literal magic.Most of the Marvel Universe was involved in this, including The Avengers, the Fantastic Four, the Runaways, and many other heroes. The X-Men comics were, by and large, uninvolved in the crossover; this is because of the decimation of the mutant population that happened at the end of House of M. However, two of them did join, both of them time travelers - Cable sided with Captain America, and Bishop joined forces with Iron Man. Marvel's cosmic heroes also stayed out of the event as most of them were dealing with the Annihilation event, though Nova was briefly involved afterwards.In the summer of 2007, Dan Slott teased readers with retconning the whole thing away in the Great Lakes Initiative/Deadpool crossover when Squirrel Girl tried to go back and prevent the Stamford explosion, which had the side effect of turning her longtime crush Robbie "Speedball" Baldwin into the brooding Penance. (She ended up in the future instead.)In December 2007, a "What If" special was released; a stranger reveals two alternate versions of Civil War to Iron Man, who is visiting Captain America's symbolic grave at Arlington. The first is "What If Captain America led all the heroes against the Registration Act?" and the second is "What if Iron Man lost the Civil War?". Additionally, because of the times the stories take place What If: Annihilation can be considered a third alternate version of the Civil War, with the Annihilation Wave reaching Earth during the climactic battle of the war and both factions join forces under Nova after he delivers a What the Hell, Hero? speech to everyone.The event's plot is used as the story in the video game Marvel Ultimate Alliance 2. Initially.
Civil War provides examples of:
Accidental Public Confession: When Wolverine was tracking Nitro, Iron Man interrupted him, and told him that a SHIELD unit is ready to deal with Nitro, that they only needed to know a place and attack... and Wolverine, without thinking before talking, had just slipped Nitro's location.
Achilles in His Tent: Namor refused to take part in the disputes of power of the surface dwellers, but finally helped Captain America in his hour of need.
Actually a Doombot: Nick Fury's whereabouts were unknown since the Secret War. Each time you saw him somewhere, it was actually a Life Model Decoy made by SHIELD (and of course, She-Hulk makes fun of this). There's an interesting twist with Sharon Carter: she has a LMD of Nick Fury at her room, everybody in SHIELD knows it's a LMD, but it's a LMD hacked by the real Nick Fury, who uses it to talk with her.
The Alcatraz: The captured superhumans are imprisoned in a large prison in the Negative Zone. Escape is "futile" since it is in a separate dimension composed of antimatter.
Anti-Villain: Captain America is a type IV, technically speaking he is the Villain.
And the Adventure Continues: The story does not have an end. It simply left the characters at their new places, were they would fight from then on.
Arson, Murder, and Jaywalking: When Speedball wakes up (after being blown up to another state and losing his powers in the process), he is told the bad news, that, because of his actions, Stamford is now a smoking crater, that all the other New Warriors are dead, that all super-humans must now register to the US government... and that he is under arrest.
Artistic License - Law: Among other things, as lawandthemultiverse.com points out, a law is not necessarily enforced as soon as it goes into effect and doesn't necessarily go into effect as soon as it's signed (it can be done that way to an extent but is extremely bad form and likely to get cases thrown out of court). Once the law is passed, it typically goes into effect on a future date, often in stages, to give both the government and the people time to prepare to comply with the law, especially if registration is part of the new law. But SHIELD has a go at arresting Captain American before it even comes up for a vote. Later they end up busting into people's houses' at 12:01 am with registration slips and arrest warrants in hand.
Lots of heroes (and villains) get arrested, but there's precious little legal process to go along with it. Alleged criminals don't get their Miranda warnings ("You have the right to remain silent" etc.), they don't get to see a lawyer in the Negative Zone, they don't get to post bail, etc... any similarity to Guantanamo Bay is a mere coincidence.
Similarly, for an experienced lawyer, She-Hulk's website takedown lawsuit goes off the rails quickly into a trial of the New Warriors. It would have been an open-and-shut case in reality. If speech creates a clear and present danger for anyone, it's illegal. Revealing the identities of superheroes and then reporting on the resulting violence against them clearly passes even this high standard. Testimony about the tragedy itself and somehow getting Iron Man to testify about the upcoming superhero registration act is irrelevant and should not have been allowed.
The Bad Guys Are Cops: Several villains are forced by the government to capture the rebel heroes. Most of them take pride of the "now I'm the cop and you're the criminal" irony.
The Bad Guy Wins: Red Skull had a simple plan: take advantage of Captain America being detained to kill him with a sniper shot and a close shot by Sharon Carter, under mental control. And it worked: Captain America is dead. At least for a while....
Bad Liar: Captain America in disguise, luring Sally Floyd into a secret room for an interview. He did not know that, in 2007, Coca-Cola was not being distributed in glass bottles anymore.
How does Captain America know that Spider-Man has really left Iron Man's side, that he's not a spy? Because Spider-Man is a very bad liar, and he would notice it if he lied to him.
Breaking the Fellowship: The Fantastic Four Four verged into this, with their own domestic civil war. Reed Richards fully supports the act, he's the big brain of it second to Stark; but the Thing opposes it and left the country, Johnny Storm is in the hospital, and Sue is so against it that she break up with Reed.
She was already around, but since this story Maria Hill became a steady and unavoidable character of the Marvel Universe.
Broken Aesop: The storyline featured the superheroes favoring registration fighting the superheroes opposing it. Apparently, the two sides were supposed to be presented evenly but due to the clear Aesops of the last century saying that secret identities are good and government oversight of superheroes is evil, it was hard to sympathize with the Pro-Regs. Especially since Iron Man, the Pro-Reg leader, became a borderline Fascist Nazibot for most of the storyline. The whole thing was basically a titanic Idiot Plot where everyone held the Conflict Ball.
The X-Men in particular stayed out of the entire debate surrounding the Super Human Registration Act since in their own comics, government registration of mutants was always portrayed as the first step towards state-sponsored internment/genocide of anyone with an X-gene.
Brother-Sister Incest: Played with. All the members of the resistance had fake civil identities. For the Invisible Woman and the Human Torch, the only thing that Nick Fury could got was the identities of a married couple. Yes, they also squicked.
But for Me, It Was Tuesday: After revealing his identity, all the enemies of Spider-Man who have ever been began to attack him. And one of them...
Spider-Man: And you are...?
Villain: Don't you remember me, Peter?
Spider-Man: I'm sorry, do I know you?
Villain: I am... Will o' the Wisp? We have fought... a pair of times?
Spider-Man: Oh, yes. And remind me, which were your powers...?
Villain: Are we really having this conversation? You really don't remember me, Peter?
Cape Busters: S.H.I.E.L.D. creates a new unit to capture heroes that refuse to register in defiance of the SHRA. In an amazing display of subtlety, they are named the "Cape Killers."
Cassandra Truth: Now that she knows that Peter Parker is Spider-Man, she wants to know how did he became Spider-Man. What? A radioactive spider? An animal totem? That was not a moment for jokes, Parker!
The Cavalry: For the final battle. First, Captain America's side use their mole to open the cells, and have the prisoners on their side. Then, Namor and his army provides further support. But Stark replied with a counter-cavalry, the new heroes of the 50 states initiative and the mechanical Thor.
Luke Cage, attacked as soon as the Act came into force, was rescued by Captain America, Daredevil and the Falcon.
Cavalry Betrayal: Sort of. Wonder Man found an Atlantean terrorist cell, and called SHIELD for reinforcements. And the reinforcement is... the Green Goblin, who began to kill all the blue guys with his bombs. Wonder Man asked to the SHIELD, What the Hell, Hero?, what kind of cavalry is that? They told him that the Green Goblin was not the cavalry, that the cavalry is still ten minutes away.
Chekhov's Gun: What is that CD with the number "42" in it? Sorry, classified information.
Chekhov's Gunman: A relative of Goliath, who wants to avenge him, and wants the secret of the Pym particle. Black Panther treated him as a Naïve Newcomer, but he got a higher role in World War Hulk.
Clark Kenting: The heroes in the resistance must stay hidden, and use new secret identities. But the Human Torch is a celebrity (in-universe), so how can he hide his face? With a pair of glasses? Reed Richards told him: that can't work.
Cliff Hanger: Issue 3 ends with the return of Thor. Or is it? In issue 4 it is revealed that it wasn't the real Thor, but a robotic clone created by Richards and Stark.
Conflict Ball: Was there any real reason for them to be fighting like that? Just one act people don't agree with, and they are at each others' throats? Even small wars do not work that way. There had to have been some underlying tension that the act finally set off (like many political hot button issues).
Granted, there is some discussion about how "tensions have been rising" for awhile, but it still doesn't make sense that so much violence happened so quickly.
Continuity Nod: Before the last battle, Iron Man pointed that he had a mole within Captain America's ranks. He told that he was already aware of that, and Iron Man did not understand how did the secret leaked. It did not: the traitor was discovered by Black Panther, in his comic book.
Continuity Snarl: Beyond the creative differences between writers, there were some minor contradictions between the main series and the tie-in comics
When Iron Man gave a tour guide to Spider-Man into the prison of the negative zone (Spider-Man comic book), he said that prisoners would stay there for all their lives, unless they signed. When Spider-Man wanted to leave the Pro-registration side and join the resistance (main crossover comic), Iron Man said that the prison was only a temporary measure.
In the first issue, Reed Richards supported Stark's projects because he made studies that confirmed that super-man activity would lead to even greater disasters. In the FF comic book he talked insted about an old uncle who had conflicts with the law. The contradiction was fixed in a later FF comic book (or planned all along), it was revealed that the alleged uncle was a lie, that he supported Stark because of his studies.
When Spider-Man joined the resistance, he took out the spider-armour (as Stark may manipulate him with it) and retrieved his classic suit. However, when he appeared in the Frontline comic book helping Ben Urich to hack into Stark's finances, he was still using the armour.
Covers Always Lie: Fantastic Four 537◊: Dr. Doom lifting Thor's hammer, over the defeated bodies of the Fantastic Four. Only a tiny and limited number of "worthy" heroes have been capable to lift it. Nobody should be surprised to find out that Dr. Doom is not among them.
Damsel in Distress: The Invisible Woman rejects the Act, even comparing it to Nazi Germany. When Richards' arguments failed, he tried to invoke the trope: he does all this to protect her. She broke the whole building to point that she does not need "protection", she's the poster girl of Took a Level in Badass.
Darker and Edgier: The story began with a fun and colorful battle of the New Warrior against a set of C-class villains, with jokes, "take that" and all the usual stuff. Then Nitro blows up, taking the whole Stamford with him, and things get increasingly darker.
Depending on the Writer: Up to and including whether holding American citizens in a concentration camp without trial after intentionally setting mass-murdering supervillains on them was a bad thing.
Developing Doomed Characters: The Thing Nº 1 has a guest appearence of Bill Foster, Goliath, a long forgotten character. You all know what happened to him a short time later...
Does This Remind You of Anything?: The first time the moment when Speedball gets shot in Civil War: Front Line is shown the panel is practically identical to the famous picture of Jack Ruby shooting Lee Harvey Oswald. Right down to the expression of pain on Speedball's face and the shooter's clothing.
The angry mother was Cindy Sheehan who protested the second Iraq war and became famous for doing so after her son was lost. Though in Sheehan's case, she was already politically active before her son deployed.
Excuse Plot: According to Word of God from Mark Millar. He just really wanted to write a story about people who were typically on the same side beating the tar out of each other, and the Super Registration Act was just a convenient backdrop he came up with to allow this to happen. Any and all political subtext was completely unintentional.
Face Fault: Not a common sight in superhero comics, but in this case it was largely justified. Spider-Man is on live television, just about to take off his mask. J.J. Jameson, the highest hater of Spider-Man in the universe, is dying to finally see his face after all those decades. "My name is Peter Parker, and I have been Spider-Man since I was 15" (if anyone needs to remember the obvious, he has also been Jameson's employee most of this time). How else could have Jonah reacted?
The Faceless: Norman Osborn, the Green Goblin, is held prisoner, but someone has allowed him to leave prison and deceive the tracking nanobots to seem as if he was still in prison. The man who helped him was Tony Stark.
The "What if... issues were introduced by a faceless manifestation of The Watcher.
False Flag Operation: In Prelude to Civil War, Iron Man hired his old enemy the Titanium Man to make an attempt on his life in order to provide a cause for not passing the registration act (America's enemies would take advantage of the division and wipe them all out).
This is the storyline that led many fans to call Tony Stark 'Der Eisenfuhrer'.
The Marvel brass really regretted not giving the Thor clone an official name right away, since the fans' decision to label it "Clor" seemed to irk them. Marvel later on named it "Ragnarok." Fans still call it Clor.
Friendly Enemy: All superheroes (and specially Captain America and Iron Man) may be going at each other's throats, but they have been friends and allies for decades.
From Bad to Worse: A band of terrorists tried to attack to Midtown school, where Peter Parker was working as teacher before revealing his identity. But the resistance (that Parker had already joined) is protecting it, and Wolverine took the terrorists. All except one, who knows how will things end if he fights against Wolverine, and run... only to be stopped by Punisher.
Genre Savvy: When the Invisible Woman, in the resistance, met Black Panther. She was happy to see him again... and then realized that, as he was comforting her for leaving her home, he was also smelling her. That he was checking her sweat or anxiety, to see if she was lying. He did not deny that, and pointed that he has been doing that with all the other members of the resistance, looking for any traitor in their ranks.
Godwin's Law: Take a drink every time someone compares the registration act to Nazi Germany, the USSR, China, the Roman Empire, or any other oppressive/totalitarian regime you can think of and you could potentially be wasted after a single issue of any given tie-in.
Heel Realization: Initially, Tony Stark simply denied any relation with the New Warriors. The reaction of Miriam Sharpe, a woman who lost her son in the explosion, made him take a more proactive role to enforce the registration act.
Living up to the trope named after him, Mr. Fantastic was the sole human on Earth who was informed about Annihilus' genocide of all life in the universe that was going on at the same time. First from the Super Skrull, a hated enemy who literally had to BEG Richards to let him use the Negative Zone portal after giving a firsthand account of Annihilus' genocide. Later Nova sent multiple distress signals to Reed, warning him that Annihilus was DAYS away from reaching Earth. Reed told no one about either of these warnings. What If? Annikilation shows just how costly that would have been.
I Need a Freaking Drink: As a former alcoholic, Sally Floyd had some of those moments when put under great tension.
Issue Drift: Ye gods. One second we have a pseudo-X-Men recycle. The next we have the biggest writers'Flame War about the Bush Administration since Family Guy's uncancellation.
It Always Rains at Funerals: Both during the funeral of Goliath, and the funeral of the cameraman that was filming the New Warriors' reality show (shown in Civil War: Frontline)
I Warned You: With the footage of the fight, Sharon Carter reminded Maria Hill that she warned her that Captain America would not accept her proposal to lead the registration act. But no, Hill thought that she knew Cap better than his old lover...
Jerkass Has a Point: In this case it's so big that it's the story ending: Captain America realizes that Iron Man had a point all along, and stops fighting.
Failed attempts by Executive Meddling to grant Iron ManKarma Houdini for his crimes during this storyline — instead of admitting how wrong (or at least over-the-top) he was — have only resulted in Flanderization and ruining an originally strong character. Not to mention that Iron Man won, retroactively validating his crimes, since the story ends with Captain America deciding to stop fighting because Iron Man had a point.
Tony and Reed are never arrested or receive any punishment for cloning Thor, resulting in the death of Bill Foster (unless you count Tony's well deserved beatdown at the hands of the real Thor).
After getting shot, nobody ever called Cap on any of the shenanigans he pulled and was later pardoned by Obama. Also, Hill, who started the whole conflict in the first place, was merely demoted to Deputy Commander.
Killed Off for Real: Only Microbe, Goliath, Goldbug and Plunderer. Captain America returned, despite Marvel's claims that Cap was definitely dead for ever and ever no matter what, and so did the other New Warriors.
Lesser of Two Evils: Iron Man admitted that he was being a bit of a jerk, but that one of the reasons he was doing all this was because the government had even worse plans: instead of making superheroes join the army, they would fill the sky with Sentinels and outlaw all superhumans. Because that worked so well in the past...
Living Lie Detector: The Black Panther checked one by one the members of the resistance, and found the traitor within them: Tigra.
Lost Aesop: The comments of Sally Floyd to Captain America. Her references to Nascar, Myspace, Youtube, etc; merely illustrate that he was out of touch with the people real interests. Meaning: during the times a guerrilla organization wages a civil war over some important issue, only a very small fraction of the population agrees with it. Most of the people want, first and foremost, to have a normal life (iconized by Nascar, Myspace, Youtube, etc) with no guerrillas around, even if they agree with the guerrilla's claim on the level of the ideas. But the Aesop was completely lost in most of the readers, as the real United States have not faced a real civil war since over a century (and certainly not a civil war like the Spanish one).
In addition, many fans believe that this "Aesop" wasn't an Aesop at all, and that rather than look sheepish and ashamed, Captain America should have responded to Floyd with some sort of "Sorry I haven't been keeping up with popular culture, lady, but I've been too busy saving the freaking planet time and time again to pay attention to the irrelevant bullshit people waste their time with."
Magic Pants: Averted. Wolverine tracked Nitro, who made a bix explosion and turned him to dust. Wolverine's healing factor rearranged him, but not his clothes: he had to fight naked. With Censor Shadows all around, but he was still fully naked.
Miranda Rights: The new Miranda Rights for a superhuman caught in illegal unregistered super-hero duty warn him that he is making an illegal use of super powers, and that he has 10 seconds or so to surrender. Of course, most of them don't do that.
Sally Floyd, accused of hiding the wereabouts of Captain America, received the standard Miranda Rights when taken prisoner. But as there was no evidence against her, she was released.
The Mole: Both sides had a mole inside the other side: Tigra was with Cap but supported Iron Man, and Pym was replaced by Hulking
Besides the Civil War itself, Sally Floyd and Ben Urich investigated Norman Osbourne, who was somehow released from prison. And, to make it more strange, the nanobots in his blood had been manipulated to make it seem as if he was still in prison; something that could only be done by a superhero of the conclave that led the registration process. Sally Floyd had a mole among them, Ms. Marvel, who told her that it was Tony Stark.
Deadpool: ...and the ripe, nubile Young Avengers! And I'm especially discomfited to admit that Wiccan and Hulkling are looking especially nubile!
Nested Story Reveal: Wonder Man fought against a Z-class villain ("C-class" is too much, it's just a harmless small guy with a mice suit), the police orders him to show his superhero ID, and then the director stopped the filming: Wonder Man was filming an advertisment.
Nice Job Breaking It, Hero: The New Warriors storming into the villain's house and causing the destruction of Stamford is almost a poster example of the trope.
Spider-Man is aware that there is popular support for Iron Man and the act, that only superheros are against it (which is the whole point of the story). So, when he turned against Iron Man, he showed up at a TV news that was airing live, and revealed Stark's big secret: that there is a prison for superhumans in the Negative zone, and that they send the villains and unregistered heroes to it. The result? Stark became even more popular.
Non-Fatal Explosions: Speedball survived the explosion. He was blasted to another state, but survived. And, of course, Nitro survives his own explosions.
Nothing Is the Same Anymore: Civil War completely redefined the status quo of super heroes. Before it, there were vigilantes that save the day and dissapear in the night, and some public groups who save the day and return to their mansion, with the occasional help or bickering of the government, military, press, secret agents or whatever. Since Civil War, everything changed: super heroes got divided into The Empire (those who work for the government) and La Résistance (those who try to keep doing thing the old fashioned way, but under severe persecution from the others).
Not in This for Your Revolution: Punisher. He's in Cap's side simply because Iron Man is using villains. But he's not selective: if other villains show up at their base, he'll kill them as well.
Black Panther: You just decided all by yourselves that you are the Earth's protectors. And that you, and only you, not your teammates or family, are trustworthy enough to include in the process... What happens when you disagree? When one of these Earth-changing moments finds you all at odds with each other, here in a secret meeting?
Number Two: Spider-Man starts off as this for the Pro-Registration side, even being the first hero to officially register live on television. He eventually defects though when he disagrees with Iron Man's morals.
Offscreen Moment of Awesome: In the final fight, as seen in the Black Panther comic book, Storm took a few rounds against the fake Thor. She took him down several times, and each time he get up for more. Then Hercules saluted her and the Invisible Woman. "Excuse me, beatiful ladies, I will continue from here". From then on, Ororo and Susan simply saw Hercules destroying offscreen the robot at his leisure, clearly without needing any help.
Tony Stark and Reed Richards claim this, due to their status as "futurists". Whether or not people call them on this depends on the writer.
On the anti-reg side, Cable, who takes the opportunity to give the President a lecture on how the Fifty States Initiative will only lead to tyranny while Deadpool is using the White House toilet.
In a meta-example, many readers would have seen Captain America as in the right no matter what he did mostly because his name is Captain America.
Captain America has consistently been one of the two main moral compasses of the Marvel Universe (the other being Spiderman). While they both have been shown to be wrong on occasion, neither has historically slipped too far from the straight and narrow. They took both these people and put them on the same, anti-registration side.
Averted with Doctor Strange, who took himself completely out of the conflict other than to side with the Anti-Registration group on principle. When questioned by Uatu the Watcher, he claimed it wasn't his to decide how superpowered humanity was going to go, and all he could do was pray for the outcome that would be best for everyone.
Plothole: Norman Osbourne is held prisoner, and for the Thunderbolts program he has nanobots in his blood that allow SHIELD to control him and track his activities. But someone messed with the nanobots, and he sneaked into a diplomatic conference with an Atlantean ambassador and fired him. But the police interrogating him want to know: nanobots or not, how did he got into a diplomatic conference with a phony ID card? How is it that the security cameras did not notice him before? And how did he got inside with a gun? All that he replied was "I can not reply" (clearly having been brainwashed into not exposing his controller), and then SHIELD came to take him, leaving the questions completely unanswered. The mastermind behind him Tony Stark would have been able to hack the cameras, but the rest is still odd.
Point of No Return: Capturing Prodigy, the first superhuman detained to enforce the Registration Act, was the "crossing of the Rubicon" for Iron Man... in a very explicit way. The comic book shows two stories for the price of one: on one side, Iron Man fights against Prodigy and starts the Civil War, and on the other side, the Roman Julius Caesar crossed the Rubicon, fully aware that by doing so he would start a civil war. Alea Iacta Est: The die has been cast!
Put on a Bus: Shortly before the event got started, the Illuminati got together and sent the Hulk offworld because they knew something bad was coming and nobody wanted to worry about him going on a rampage in the middle of everything else. This wound up starting the Planet Hulk storyline.
Read The Fine Print: Wonder Man is a registered super hero. Agents of SHIELD gave him a stealth mission, to follow an Atlantean guy and see what is he up to. Simon says that he never signed to be an agent of SHIELD. Poor misinformed soul: as they pointed him, that is precisely what he signed for!
The Real Heroes: Pops up right at the end. Ironically, it's because of them that Cap surrenders, and we all know what happened later.
Red Eyes, Take Warning: Good work Namorita, you have just slammed a living atomic bomb to a school bus, and ordered him to surrender. Hey, wait, why are his eyes red now...?
Revealing Skill: A fight interrupted by a lighting bolt is followed by the return of Thor. But not the real Thor, it was a robot Thor
Revisiting The Roots: In-universe. The Thing did not want to take sides, and left the United States, moving to France. Once in Paris, a local superhero team request his help for a grave crisis. So what now? A secret government agency that turns against its people? A multinational conspiracy? A war between superheroes? No, it's the "empereur le monde souterrain", a French expy of the Mole Man, who threatens to destroy Paris with his underground rocky creatures. Snif. Like in Ye Goode Olde Days of Black and White Morality of The Silver Age of Comic Books
Siege is thought of as Civil War without the moral ambiguity, with Norman Osborn and supervillains taking the place of Iron Man and other Pro-Reg characters.
The X-FamilyCrossoverSchism is also compared to Civil War for being a morally grey conflict, this one seeing more success in making each viewpoint defensible (with their home under attack and only junior members around to defend it, Cyclops wants to make a stand, which the kids are willing to do even though they know not everyone will survive; while Wolverine doesn't like them getting mixed up in this and wants to retreat).
Superman Stays Out of Gotham: Turned on its head when the X-Men Lampshade how anti-mutant sentiment was never on the radar of the heavy hitters in the superhero community (comparing the Stamford disaster to the Genosha massacre which no superheroes helped with) and declare they're staying out of the whole mess. Likely due to the X-Books' constant theme of mutant registration being the first step to anti-mutant genocide not jiving with the "Pro-Reg is right" message.
The Sentry is formally part of the registration side, but it was described at the Avengers issue that he could win the war all by himself, and so refuses to take an active part in it.
Super Window Jump: Captain America, escaping from SHIELD. And he jumped from the hellicarrier, which is flying in the sky. And without any flying heroes around. He simply had the luck that one of SHIELD's planes was flying by that place at that moment.
Mysterio II: The original Mysterio was all tricks and special effects, but you fight against Francis Klum now, and my tleportatons powers will prove to be more than...
Mysterio I:Blah Blah Blah. He loves the sounds of his own voice. Fortunately, I have a volume control. Spider-Man will be lucky if this jerk does not kill him of boredom
Switching P.O.V.: After the big fight where Goliath died, several heroes were captured, and had to be transported across the street in a military convoy. The resistance tried to liberate to prisoners. This incident (unmentioned in the main story) was seen at the Fantastic Four and Spider-Man comic books, in each case from the point of view of The Thing and Spider-Man.
Technobabble: The Radioactive Man was hearing Tony Stark and Reed Richards lost in their technobabble about the "42" prison. At one point, he mentioned that he was a bit satisfied that the US was following China's steps. When they rejected the idea, he pointed:
Captain America. You want to capture and imprison Captain America. Say those words aloud, weight their meaning, and tell me again that I'm exaggerating.
That Man Is Dead: "Robbie Baldwin is dead. Speedball is dead. It's time for Penance"
There Was a Door: Inverted by Spider-Man. Sally Floyd did not understand how did Spider-Man got inside her house, if her window is close. Easy, he used the front door.
To Be Lawful or Good: Almost everyone in the superhero community is caught into this ethical dilemma, but the two characters who take most of the cake are Captain America and Iron Man. (However, the Xmen and Doctor Strangetake a third option and stay out of the conflict.) The pro-registration side believes that their way is lawful and good, but of course the other side disagrees.
To Catch Heroes Hire Villains: They empowered the Thunderbolts to go after heroes who refused registration. Thunderbolts under the command of Norman Osborn. Including Bullseye, whose personal body count is probably well in excess of those killed in the Stanford explosion. To their credit, the pro-registration side does attempt to keep the Thunderbolts on a tight leash.
What the Hell, Hero?: Twice in the above mentioned Civil War: Frontline. The intrepid reporters Ben Urich and Sally Floyd go to interview Captain America and Ms. Floyd proceeds to chastise him for his reckless superheroics. Then they pay a visit to Tony Stark and reveal that they have discovered that he turned Norman Osborn into a Manchurian Agent, and made him attack an Atlantean ambassador in order to create tensions between Atlantis and the United States, so that the US government would be compelled to grant military contracts to Stark, which would boost his corporation's stock value, and the profits from which he could use to fund the Avengers Initiative program. This revelation lead to Tony Stark's hilarious reaction.
In What If: Annihilation, Nova does this to everyone on both sides for arguing and fighting each other over a law and their identities when galacticl civilization was on the brink of extinction.