The amount of superheroes who have died at some point in their comic book career is shockingly high. However, the number of supervillains who have killed superheroes is comparatively low. Heroes die though all sorts of different means. They're often the subject of a heroic sacrifice, and they routinely kill each other. Seriously, superheroes kill people all the time.
But incidents where superheroes are killed by their villains are actually pretty rare. One might think this would be the most obvious way for a costumed crime-fighter to go out, but it seems either supervillains are incompetent, or comic book writers can’t find many ways to make getting murdered look heroic.
The pages of Marvel Comics are rife with amazing and deadly villains. Bad guys like Loki, Doctor Doom, the Red Skull, and Kingpin all have intimidating reputations (and rightfully so), but that doesn’t mean they’ve managed to actually kill their rival heroes. In the Marvel universe, antagonists often seem to come up just short of gaining their ultimate vengeance. However, every so often, a supervillain gets lucky and actually manages to cut down a superhero. It’s so rare, it's a tragic surprise each time it happens.
The death of Elektra, in Daredevil #181, is one of the most infamous moments in Marvel Comics history, and it was incredibly graphic for that time period. Daredevil’s former love interest, Elektra, was facing off against his antagonist Bullseye due to a professional rivalry. Readers everywhere were shocked when the murderous Bullseye gained the upper hand, and ran Elektra through with her own sai.
Elektra survived long enough to drag herself to Matt Murdock’s doorstep, before dying in his arms. She wouldn’t be dead for long, however, as ninja resurrections became kind of her “thing.”
Marvel made quite a big deal about the milestone issue of Amazing Spider-Man #700, which was the culmination of the "Dying Wish" storyline. Still, nobody expected the results to be so... extreme. Long-time Spider-Man foe Doctor Octopus, dying a slow death, was able to swap his mind with Peter Parker’s, taking over the body of Spider-Man and leaving his opponent to die in a decrepit shell.
Before Peter died in Ock’s body, he managed to force Otto to live through his lifetime of memories, which helped the former villain set out on a righteous path as the Superior Spider-Man. Doc Ock would hold the title for more than a year, before Parker inevitably returned.
The comic book Civil War was a hard-fought and bitter conflict that saw Captain America and Iron Man duking it out over the Superhuman Registration Act. Cap took his forces underground to fight the government’s new rules, and Iron Man hunted him with all of his resources. This eventually led to an all-out battle between the two sides, before Cap ended it all by surrendering himself.
Things took a turn for the tragic in The Death of Captain America when, on the way up the courthouse steps, Captain America was sniped in the back by long-time minor antagonist Crossbones. To make matters worse, another villain, Doctor Faustus, had brainwashed Cap’s girlfriend, Sharon Carter, resulting in her finishing off the First Avenger with several shots to the stomach. Steve Rogers, of course, returned in due time.
Grant Morrison’s lengthy run on New X-Men was chock full of weird plots and bizarre twists, and the series’ climax was no exception. One of the team’s new allies, Xorn, was revealed to be Magneto in disguise, in what is still an incredibly controversial, and currently retconned, development.
Magneto set the X-Men up for a great fall, and his attack on them included giving the powerful psychic Jean Grey a magnetic aneurysm. This quickly killed the founding X-Man, but it also sent Wolverine into a rage, and he beheaded Xorneto. The Xorn stuff was eventually written out of continuity, but Jean Grey has remained dead, despite a time-traveling younger version of herself showing up.