Flash Forward the Marvel Universe to about thirty years in the future. Aaron Stack, the Machine Man, is awakened by a monolith. The black slab rips away his synthetic skin and human appearance and transports him to a lost city on the moon. There he is greeted by Uatu, The Watcher, who has been blinded. There, Aaron is told that he is to be the new Watcher, and to release all aspirations to be human.Meanwhile on Earth, civilization has crumbled, and prominent heroes as well as villains across the world have risen to power to save their nations. America is under the control of Norman Osborn, the Goblin King. Across the world, people are enslaved to the parasitic Hydra. Tony Stark has armored himself in a sanitary skyscraper. Half of the Fantastic Four are dead. Marching up to the streets of New York is the mysterious Skull, who has built an army by controlling all he meets.Oh, and everyone (and we mean literally EVERYONE on Earth) has super-powers. Nobody knows why.And thus begins a journey from the dawn of the universe to its twilight, exploring the themes of heroism, empowerment, life, death, afterlife, and the cosmos.Written by Jim Krueger and drawn by John Paul Leon, with ideas from Alex Ross' sketchpad. It has two sequels, Universe X and Paradise X.
One minor detail that did get incorporated into the main Verse is that the 2001 monolith from Machine Man's origin story was a Celestial gizmo. In the last issue of his 1990's series, the Celestials take him away into space using a monolith.
Infecting Earth's population with the Terrigen Mists to turn everyone into Inhumans has been done twice in the Mainstream universe- during War of Kings and now during Inhumanity. We are sure it's an alternate continuity, right?
Always a Bigger Fish: At the beginning of chapter 12, the Celestials tower over the skyline of New York City. At the end of chapter 12, Galactus towers over the Celestials, looking big enough to literally munch the Earth in one bite. When he actually fights them, he's reverted to a smaller form, but he still turns out to outpower them.
Assimilation Plot: Before the start of the comic, much of the Inhuman population began leaving the Hidden City and Black Bolt along with Inhuman Royal family planned on leaving for space. Black Bolt knowing many of them would be weakened by the pollutants outside of the Inhuman home and targeted as being mutants or being too different, decides to release a weapon, of his brother Maximus' design, that would release Terrigen Mists all over the world mutating the entire population of the world so that no one would be able to tell who was originally human, Inhuman, a regular mutant or not.
Batman Gambit: Magneto calls his Brotherhood "Evil", which places the X-Men as being the judges of Mutanity, at the same time portraying Xavier as a bigot, thus winning converts by the score around the world.
Doing in the Scientist: The Marvel universe mutants never really squared up with science to begin with, but in this continuity they're the result of experimentation by the godlike Celestials. The above case of killing the wizard is also, oddly, an example of this, because the means by which they became Sufficiently Advanced Alien Shapeshifers is also by Celestial manipulation.
The Dog Bites Back: When Toad and Magneto involuntarily exchange powers, the former becomes one of the mightiest mutants on Earth, outsts the latter from control of Sentinel City and makes him his personal court jester, abusing him every chance he had.
"Why did they hide? Wouldn't they be treated as gods?" "Yes. But mankind always turns on its gods. Isn't that right, Uatu?" "And I wondered... could a goddess lose her faith? And what does a goddess put her faith in?" "The Celestials made us gods, so who do we pray to now?" "(Hank) Pym's first creation as a god was to make a monster."
Godiva Hair: Medusa, several times. (Later averted for no apparent reason, all things considered. Scenery Censor with shadows replaces it.)
Homage: Inspired by Aaron/Machine Man's origins in the 2001 comic book, and the theme of human evolution, there are several homages to 2001: A Space Odyssey, most notably when Aaron wakes up to find a monolith at the foot of his bed.
Merlin and Nimue: The backstory shows this relationship between Doctor Strange and Clea. Clea got fed up with being Strange's student, decided he was just using her for sex, then betrayed and killed him.
Meta Origin: It's all the Celestials' fault. Everything in the universe.
But it should be stated that pretty much every character's altered appearance is meant to be a Mythology Gag of some sort. For instance, the fact that half of Namor's body is now on fire is apparently a reference to the original, Golden Age Human Torch. Alex Ross had depicted a fight between Torch and Namor in his Marvels series.
Retcanon: The plot point of Black Bolt releasing the Terrigen Mist across the globe to create a new race of human/Inhuman hybrids was later brought into the mainstream Marvel canon during Infinity and its follow-up, Inhumanity.
Winged Humanoid: Wyatt Wingfoot/Red Wing, Luna, as well as many other unnamed characters.
Writer on Board: A mild case, but you get the feeling that all involved (especially Alex Ross) really don't like Wolverine.
Also, Peter Parker's One True Love was Gwen Stacey, and he only married Mary Jane out of guilt. Explored further in the sequel series, which had Peter Parker's "perfect world" depicted as one where he was married to Gwen with a son named Ben, rather than what happened in his real life where he married MJ and had a daughter May (who was this reality's Venom). Again, another mild case but you do get the feeling that the creators (again, especially Alex Ross) definitely had their own feelings on who Spider-Man's OTP was.
Universe X contains examples of:
Autocannibalism: Multiple Man eats a duplicate of himself while lost in the frozen wilderness. This results in him becoming the new Wendigo.
Batman Gambit: Mephisto offers the key to Limbo to Cap, knowing full well that Cap will throw it back in his face, sending Belasco back in time to his first appearance in the Savage Land.
Color-Coded for Your Convenience: The Marvels of the dead who don't know they're deceased have their costume colors rendered negative. Those who do know - and have ascended to Paradise - retain their natural color. Usually, anyway.
Dead to Begin With: The many dead heroes fight for paradise. They can only be defeated if they believe they're alive.
Also, Moon Knight, Marlene Alraune, the Living Mummy, and everyone else brought back by the Reanimator Stone. They just never knew it.
Death Seeker: In addition to Daredevil, there's Marc Spector/Moon Knight, the Sons of Set, and by extension, Red Ronin and the Tong of Creel.
Also; "He was hidden with the person I would least likely be thought to ally with. I put him in the place people would never think to look. I gave him to the man who killed Susan's brother. I gave him to the man who killed Susan's brother. I gave your son to Namor, king of Atlantis. And hid him far beneath the eyes of man."
Lawyer-Friendly Cameo: A particularly convoluted example—Rom (the Spaceknight, not the Ferengi) is a Marvel character, but he was originally created as a toy—which flopped. But the rights to the character have reverted to the toy creator anyway. Rom appears de-cyborged in Limbo using the chestpiece of his cyborg armor as a shield, and is referred to only as "the greatest of the Spaceknights".
Loss of Identity: This is what happened to Asgardians before they were Asgardians, and what would happen to Earth.
Lotus-Eater Machine: Spiders-Man traps Peter in a world where he actually saved Gwen's life. For a while, he doesn't want to leave.
Petting Zoo People: Black Panther, Wakanda's Ani-Men, Dog-Face of the new X-Men, Ka-Zar and Shanna, and many others of the mutated humanity.
Pro-Human Transhuman: Once the truth about humanity being genetically manipulated by the Celestials and mutated by Terrigen mists is revealed, Richards creates massive torches to burn the mists out of the atmosphere to allow people to become human and fertile again. Inhumanity does not like this, and starts destroying the torches.
Rock Beats Laser: Eons ago on the moon (long story), the primitive Kree slaughtered the peace-loving, star-crossing Skrulls.
Superman Stays Out of Gotham: An interesting attempt to justify one of the bigger examples of this in the Marvel Universe; one charater suggests that the reason the X-Men and the other superheroes kept on butting heads rather than working together more often is that the major dark forces of the world- strongly implied to include Mephisto, and other such demonic entities- manipulated events to play up anti-mutant prejudices so as to keep them apart.
Batman Gambit: Aaron/X-51 plucks heroes and villains out of alternate realities to warn other Reed Richards' about the growing Celestials in their planets' cores. The Watchers come out of hiding to judge Uatu, and Aaron sends them to alternate worlds (by way of portal-spamming) to let those Earths know that they are being watched, thus setting the infinite war against the Celestials in motion.
Another one; Thor, Loki, Dr. Strange and Xen trek to Asgard to find Clea. When they get to Yggdrasil, they find out that she's in Hel. Odin then appears, and they make a deal, trading one of their band in Clea's place (them's the rules). Loki volunteers to be the substitute, but Odin rejects the offer, and chooses to take Thor instead. After returning to earth and killing zombie Fin Fang Foom, Thor teleports back, revealing that he had freed everyone in Hel with a speech, and that was the plan all along. If it was Loki who did it, they wouldn't have believed him. But Thor... who wouldn't believe Thor? As Loki put it; "Ain't I a stinker?"
Progressively Prettier: Jude's features look softer after it is revealed that he is not malicious, and only spreads entropy as his own measure of mercy.
Scenery Censor: Angel Steve always has an American flag curled around his body. It's just floating there, right above his groin.
Shooting Superman: Fully lampshaded in the last issue, with Hyperion standing in for Superman. Especially egregious because all parties are already dead and in an afterlife dimension.
Stripperiffic: As usual in comics, but applied more than usual to the males as well. See Lens Flare Censor above; also, Captain America in his angelic incarnation has only a strip of red-and-white bunting that streams around his body at a distance.