The Ultimate Universe was once a very popular alternate timeline for Marvel Comics. Its success was instrumental in the publisher moving out of bankruptcy in the late 1990s. At the same time, the Ultimate Universe is also known for its many divergences from the mainstream Marvel Universe, especially in tone.
Meant to bring Marvel's iconic heroes and villains into a more modern, realistic world, the Ultimate Universe sometimes portrayed this through dark means. Brutal origin revisions, changed characterizations, and outright cannibalism were just some of the universe's most notable moments. Some of these were more ruthless than others, making Ultimate Marvel the place to see major heroes taken in much more dour directions.
10 Ultimate Iron Man
Ultimate Iron Man changed a lot about the character, largely owing to how unpopular he was at the time. Instead of his usual warzone origins, Tony Stark was an experiment that represented living technology. This gave the character something of a body horror element, which was far different from what fans expected.
On top of that, the story as a whole had a somewhat bleak and mostly joyless tone. It even featured a young Obadiah Stane killing two other children and passing it off as suicide. Due to the series' contentious nature, it was retconned as a false origin for Iron Man in the Ultimate Universe.
9 The Ultimates
The third publication involving the Ultimate Universe, The Ultimates was the universe's equivalent to the Avengers. Many versions of these characters ran at the same time, allowing for wildly divergent takes on them in the Ultimate Universe. The Ultimates emphasized this with a team that was most certainly not led by "your father's Captain America."
The Ultimates had a brutal and cinematic tone that exemplified how cool and edgy it was compared to the Avengers' more old-hat and forgettable old-school adventures. Captain America was far from a paragon, Hulk was a true monster and Thor was a radical hippie whose godhood was highly suspect. Needless to say, it made Kurt Busiek's concurrent run on The Avengers look like an after-school special.
8 Ultimate Origins
Ultimate Origins fittingly portrayed the backstory of the Ultimate Universe, which was far less extensive than the sprawling mainstream Marvel history. The truth behind the connection between Spider-Man's father Richard Parker and the Hulk was revealed, all while the conspiratorial rise of mutants was expounded upon. Instead of the birth of gods, it was the dawn of Übermensch.
Perhaps the darkest part of the story comes during the end, where Nick Fury (who was shown being tortured earlier in the story) saves an African man from the same fate. This lowly character is actually Ultimate Black Panther, who has next to none of his mainstream regal reverence. This solidified that the Ultimate Universe wasn't kind to certain iconic heroes.
7 Ultimate Comics: Avengers #1-6
Set after Ultimatum, Ultimate Comics: Avengers saw the Ultimate Universe's main heroes form a new team. Though the name was more like the 616 Universe, the somewhat cynical vibe of the original Ultimates remained. This was best shown in Ultimate Red Skull, who had a much darker origin than even his Nazi counterpart.
In the Ultimate Universe, Red Skull was the illegitimate son of Captain America. The story fittingly treated such a scandal in hushed tones, with Red Skull also having immense brutality to go along with his enhanced faculties. Given that it made Captain America's son his worst enemy, the storyline was a great example of how certain properties were turned upside down in the alternate universe.
6 Ultimate Comics: Captain America
Red Skull was twisted to new levels, but so was another version of Captain America. In Ultimate Comics: Captain America, Steve Rogers learns of failed attempts to recreate the Super Soldier program. One of these was the "1960s Captain America," which was a combination of 616 Nuke and the Captain America of the 1950s.
This evil Frank Simpson tortured Captain America and tried to turn him against his home country. It was a darker take on a character who, while usually an adversary, was also at least somewhat understandable and tragic. The nihilism on display was perfectly suited to the Ultimate Universe and its less happy-go-lucky Captain America.
5 Ultimate X-Men: Tempest
The "Tempest" story arc introduced the Ultimate Universe version of the sadistic X-Men villain Mr. Sinister. Far from the flamboyant scientist of the 616 Universe, here he was a merciless serial killer who hunted down mutants. Even his appearance reflected this, with his gaudy Dracula costume replaced with street clothes and tattoos.
It's infamous for the scene in which Sinister "defeats" Professor Xavier by simply throwing him down a flight of stairs. The story also sewed the seeds for a much different Sinister/Apocalypse relationship, with the Ultimate Universe changing things drastically. For those seeking a more "cartoony" take on Sinister or even his loyal Nasty Boys, this story was the farthest thing from Chris Claremont's X-Men run.
4 Ultimate Enemy: Doomsday
Doomsday was the third art of the Ultimate Enemy trilogy, and it made a major change to a classic hero. This was the story in which Ultimate Universe Reed Richards officially became the villainous Maker. Easily one of the most iconic parts of the Ultimate Universe, The Maker is currently resetting his homeworld in the events of Ultimate Invasion.
Reed Richards has always been a member of the Fantastic Four, the group and comic book that catapulted Marvel to stardom during the Silver Age of Comics. Thus, making Ultimate Reed into a misanthropic villain was itself the "ultimate" deconstruction of this legacy. Given that the Ultimate Fantastic Four comic book was at least somewhat similar to its classic counterpart, this made the development even more tragic.
3 Death of Spider-Man
Ultimate Spider-Man was easily the biggest success story of the Ultimate Universe, and it also had the most in common with its classic counterpart. Thus, when Ultimate Peter Parker died in 2011, it marked the end of an era for the world. Dying in battle against Green Goblin and the Sinister Six, the Ultimate Universe's brightest hero met his end.
It of course led to the introduction of Miles Morales and inspired the animated movie Spider-Man: Into the Spider-Verse. Still, it was a dark and brutal story that ripped out the Ultimate Universe's heart. Even Peter's spiritual reunion with Uncle Ben felt incredibly sad and bittersweet.
2 Ultimates 3
Seen as a vast decrease in quality from its two predecessors, Ultimates 3 was in many readers' eyes the beginning of the end for the Ultimate Universe's popularity. It read like a parody of the shared universe's dark tone, with Iron Man and Black Widow having a leaked sex tape while Wolverine learned of similar liaisons between Scarlet Witch and Quicksilver.
Ultron's introduction was poorly received, and the further character assassination of Hank Pym only made things worse. Characters were written inconsistently from previous portrayals, and this made an already bad story worse. Sadly, it was a sign of things to come for the Ultimate Universe.
1 Ultimatum
When it came to shock value merely for the sake of it, Ultimatum had that in spades. Characters were mercilessly killed off, with one infamous scene showing the mutant Blob eating Wasp. There was ample brutality on display, to the point where the try-hard storyline was impossible to take seriously.
Worst of all was that the revelation behind the truth of the mutants was given in the story. This meant that an actually cool divergence from the mainstream universe was lost amid a storm of cannibalism, gore, debauchery, and bad storytelling. No other story in the Ultimate Universe was as dark—and that's definitely a good thing.