As an answer to DC Comics Elseworlds tale Kingdom Come which featured the competition's heroes some 30 years in the future, Alex Ross (the artist of Kingdom) and Jim Krueger teamed up and did the Marvel equivalent. The difference being while Kingdom Come was a 4 book series, Earth X was a three part trilogy that spanned 3 years (from late 1999-early 2004) totaling to 54 issues. It is by far one of the most extensive & continuity heavy Marvel tales ever, covering material from Marvel's humble beginning to its most recent storylines.
(Earth X #0-12 & #X) The entire world has mutated due to the release of Terrigen Mists into the air. Uatu, the now blind Watcher, recruits Aaron Stack to be his eyes and inform him of what is happening on Earth.
X-51 finds that in this new world where everyone has super human abilities, a young man named the Skull is attempting to take over the world, and Captain America and a band of other former champions of Earth have rallied together to stop him.
But there is more going on here than meets the eye; it is learned that the Celestials have manipulated the people of Earth into being anti-bodies for a Celestial Embryo that is growing at the Earth's core. With humanity in a state of mutation that is not destined to happen for another 300 years, the Celestials come to cleanse the human race from the face of the Earth.
Only the intervention of Reed Richards, Black Bolt, and Galactus (who is now Franklin Richards) stops the Celestials & destroys the Celestial growing at the center of the Earth.
At the end of the battle, Galactus returns to space, and Reed has giant "Human Torches" built around the Earth to burn the Terrigen Mists out of the air in an attempt to return Humanity back to their former state.
But this is not the end of the battle, as Captain Marvel has come to Reed Richards in a dream telling him that he will return and there is much more work to be done.
(Universe X #0-12 #X, & Universe X Specials: 4, Spidey, Beasts & Iron Men) 3 Years later, Captain Marvel is reborn through Him & Her, while he also mounts an army in the Realm of the Dead to over throw Death. While in the land of the Living Mar-Vell travels across the world with Captain America seeking the fragmented portions of the Cosmic Consciousness & other items of great power.
During their quest, Immortus & the illusive Mr. Church (who is really Mephisto) are the opposition to Richard's plan to burn the Terrigen Mists out of the air, and have started a religious following who believe that mutantity was destined for the stars.
To make matters worse, the destruction of the Celestial embryo in the Earth has shifted the Earth's mass due to the loss of Vibranium in it's core, and the world is on the brink of destruction as it's pole slowly change.
In the end, Mar-Vell collects enough power to destroy Death, & defeat Mephisto and begin building his own Paradise.
On Earth, Mar-Vell assists the heroes into convincing the newly revived Absorbing Man into becoming Vibranium and saving the Earth.
(The Heralds #1-3, Paradise X 0-12 & Paradise X Specials: Xen, Devils, Ragnarok, & A) With Death dead, nobody on Earth is dying, and Mephisto has returned only to increase those living in eternal agony. Earth's heroes must team up one more time to find a new Death.
While in the Realm of the Dead, a number of heroes are turned into the Avenging Host to assist Mar-Vell in bringing new souls to Paradise. However, the result of each new being is threatening to destroy the Negative Zone.
With a new Death, the heroes go to Mar-Vell's paradise to stop him from destroying the known universe as his paradise grows. What first appears to be the final salvo in the Kree invasion of the universe, turns out that Paradise was a way to create a barrier that would stop the Celestials and the Elders of the Universe from using the people of the universe as their pawns.
Mar-Vell gives the power of the cosmic consciousness to Reed Richards, believing he is the only man who would be able to use it constructively.
It is said that in the universe that existed before what became the Marvel universe, was one of pure cosmic awareness. This perfect universe however was threatened by the alien race that eventually became known as the Celestials.
These creatures modified themselves to the point where they had almost lost all self identity, and constructed gigantic bodies of armor out of a metal that is known as Vibranium on Earth. Their only means of reproducing was to "impregnate" a fertile planet with a portion of their energy. This energy in turn would feed off the planets energies and soon become a Celestial themselves. The planets core is also infused with Vibranium that would then become the newborn Celestial's armor. The indigenous life forms of the planet would then be manipulated so that over time they would mutate and gain extraordinary powers so that they could act as unwitting anti-bodies to the young Celestial growing inside their homeworld.
With nothing to keep the Celestials in check, the universe soon went into disorder, causing it to begin to break down. On the planet named Taa (also manipulated by the Celestials) a young being named Galen was empowered by the powerful Enigma force which turned him into Galactus (the Enigma force coming from Galactus' self in the far future where he has been turned into a star by Reed Richards) who then became the great balancer.
Because the Watchers (specifically Uatu's father) allowed this to happen, the Celestials used the Watcher's code of "non-involvement" to make them their slaves.
Eventually, the old universe was destroyed, and in the big bang, all it's knowledge was broken into pieces and scattered across existence, into a power supply which eventually became known as the Cosmic Consciousness.
The few survivors from the old universe (The Watcher, The Collector, The Grandmaster, Death, The In-Betweener, & Phoenix to name a few) survived it's destruction, and began planning to recollect the splintered fragments of their old universe and restore it to it's former glory.
While they planned this, The Celestials & Galactus went ever on, checking and balancing each other for Eons.
According to the Earth X trilogy, the Celestial manipulation of living creatures gives them special abilities. In their manipulations, to simplify the nature of the mutation, occurs in three tiers. These tiers occur gradually over time, and can be set off by any number of things.
Tier #1: Individual mutation. Whatever sets off the dormant Celestial seed in the individual causes a mutation that is unique to the being it's occurring to in relation to what set off the mutable seed. For example, in the mainstream Marvel Universe, all of Earth's super-beings are in their first tier of mutation. On Earth any number of things can set this off. Radiated spiders, gamma bombs & even puberty.
Tier #2: Is a level in which the collective beings of a planet have one specific ability. For example, the Skrulls are in their second tier, as they all bear the same resemblance and have the same abilities.
Tier #3: Is a failsafe for the Celestials, should the beings they manipulated try to overthrow their masters. The third tier is a loss of identity, in this state the manipulated beings lose all individual characteristic and are very difficult to see. However, these beings can be shaped into whatever it is believed of anything they encounter. According to Earth X, The Asgardians, The Olympians, and even Mephisto are beings who were in their third tier of mutation who's very existence is shaped by mankind's belief that they what they are.
Throw Backs: There are a number of members of the human race, that while in their first tier of mutation have abilities and appearances that are akin to man before they were manipulated by the Celestials. These are beings like Sasquatch, Wendigo, Man-Wolf and other mutations in which the being becomes almost lycanthropic in nature.
Note: Although there are three levels of mutation listed above, it has been said that there really is none, that each level is really a learning curve to one essentially great power in each manipulated being. This power is run by ones belief, and works almost at a subconscious level, and the belief in these abilities starts with the individual but then grows into the collective belief of an entire race of people. So, on a certain level, Peter Parker got his spider-powers because that's what he believed he'd get from a radioactive spider-bite, that the Things mutation was the cause of his self loathing. Bruce Banners from his pent up rage. etc.
In the Earth X story, there is a missing link, a splinter group of humanity that managed to escape the Celestial's mutations. There are two clans that are mentioned, The Moon Tribe (who worshiped the moon) & the Bear Tribe (who worshiped the bear) these missing links of humanity became hunted and killed by the genetically manipulated humanity. However, packs of them managed to survive.
Wolverine, who for years though he was a mutant, is a descendant from this tribe, and is actually a true human being. The natural evolution of a human in the Earth X universe is to adapt to their environment, and eventually evolve to defend themselves. At least the Moon tribe eventually developed a healing factor (to cope with the diseases that Celestial manipulated man brought with them) and claws out of bone for defense.
In Earth X, it is revealed that Mephisto was the product of the Celestials first manipulations of people on Earth. These early creatures were very susceptible to the third tier of mutation, and eventual became the demons that Price Wayfinder & his crew battled when they arrived in pre-historic Earth.
The being that became Mephisto was though to be the devil and that's what he became. Believing that there would be a final judgement when time came to an end, Mephisto decided to come up with a plan that wouldn't spoil his fun. He soon learned that time travel was possible, however, if you didn't travel across the right path it would create an alternate reality, where anything you may do would happen outside of the universe that you left. Mephisto used the idea of time travel as a way to tempt people into creating these alternate realities.
With these alternate realities created, Mephisto would have a new playground, and new people to manipulate and most importantly, he'd be able to escape the final judgement he believed was waiting for him at the end of time.
Thanks to Mephisto's manipulations, the elders of the universe had an even more difficult time collecting the fragments of their own universe.
Death was given the job of manning the collecting pool of reality. With the advent of alternate realities somebody had to take these fragments and put them together. And thus death was born. The realm of the dead is nothing more than an echo of memories past, because it is a collection of the fragments of dead alternate realities. These dead fragments echo the life it still feels from it's alternate counterparts.
When Captain Marvel slew death, little did he realize how badly he upset the nature of the universe, because nobody would die.