Marvel’s Civil War was one of the most devastating events in the history of the company, but, according to the initial story draft, it was supposed to be even more traumatic, all thanks to Tony Stark. Drawn in Steve McNiven's hyper-detailed style and written by Mark Millar, a well-known proponent of darker story tropes in mainstream comics, Civil War set a standard of production across the industry at the time for scope, scale and visual spectacle. However, the story was at first outlined to have even greater permanent consequences, as Iron Man, leader of the Pro-Registration side, was originally set to use stolen tech from Doctor Doom to depower captured heroes on Cap’s side, including Steve Rogers himself!
Though the history of the Marvel Universe has followed its heroes through many a twist and turn, few events have had the kind of lasting impact as the seminal 2006-2007 hero-versus-hero throwdown known as Civil War. Begun when the villain Nitro let loose an explosion that killed a group of schoolchildren while fighting the inexperienced hero Speedball and his Z-list team the New Warriors, Civil War encompassed almost the entire Marvel line and resulted in a multitude of heroes, including Speedball, being detained by the United States Government, with another large faction being forced into hiding as fugitives. With the fallout ranging from the death of Captain America to Spider-Man’s identity being revealed to the public, Civil War set a new standard for crossover events which left a lasting mark.
However, the original plot beats would have left an even greater legacy. On his personal blog, The Tom Brevoort Experience, former Marvel Executive Editor shared Millar’s original pitch, and the results were even darker than the final draft. In the original version, Iron Man didn't stop at imprisoning his friends, instead using stolen technology to forcibly depower heroes who refused to submit to registration. Described as “a half-finished device Doctor Doom was working on which turns super-people into ordinary human beings,” Millar’s plan was to have this technology be “used as a kind of superhero electric chair." He wrote:
This is being used on Speedball, the hero who kicked this whole thing off, and we see him stripped of his superpowers on live TV and returned to society. It should be an awesome moment and one the heroes watch with a certain amount of fear.
Civil War Was Going to Depower Captain America
In the final version of the story, Speedball is the only survivor of the massacre in Stamford, and is arrested by the government-loyal heroes led by Mr. Fantastic and Iron Man, leading to his incarceration. While he was not stripped of his powers, he was for a time only be able to use them when triggered by pain, leading to the character taking on a new persona as Penance and joining the villain team the Thunderbolts.
The outline goes on to describe how a government official would take control of the machine, intending to depower all Marvel's heroes, and be stopped by Captain America, who would lose his powers in the attempt. This story beat wasn't used in the crossover, but Steve was 'assassinated' following Civil War (actually sent tumbling through time), and later lost the powers granted to him by the super soldier serum, showing that the idea splintered into different forms, with Civil War ultimately taking Cap off the board in a different way.
Civil War Would've Been Even Darker
Millar is known for his dark, but stylish and dramatic style of action, and Civil War saw him criticized for many plot points derided as contrived or out-of-character, such as Spider-Man unmasking and the appearance of a robot Thor whose strength matched the real one. However, this particular change would have done even more to make Iron Man the obvious villain in the story, as it would have changed him into a much greater totalitarian threat. Arresting rogue superpowered individuals in an effort to deter violence is debatably an acceptable solution, but robbing them of their individual powers, in many cases their very identities, has an overtly fascist subtext that could have made Civil War the death knell for Tony Stark's time as a true hero.
Source: The Tom Brevoort Experience