Page 2-4
The three characters standing here are Dr. Strange, Dr. Doom and the Molecule Man. Dr. Doom has been working in secret to attempt to stop the Beyonders from destroying everything. The incursions are Dr. Doom’s fault. When the Black Swan first appears in New Avengers, she refers to a godlike entity called “Rabum Alal.” This was, in fact, Doom himself. Dr. Doom has been behind the incursions the entire time.
It started with an experiment conducted by an all-powerful race of beings called the Beyonders. They wanted to see what would happen when they destroyed all life simultaneously. Doom was the first to learn of this plan, and to learn of how they were going to do it: using the abilities of one of the most powerful beings on Earth: the Molecule Man. The Molecule Man can literally change any molecule in existence, including his own or external molecules, into anything else. He had to impose a series of mental blocks on himself to keep from destroying all reality. The Beyonders are simply removing the blocks…on a timer, set 25 years ahead of time, at which point the Molecule Man in each distinct reality will cause its universe to detonate. Significantly: the Molecule Man is a universal constant; while most of the heroes and villains in the Marvel Multiverse are different across the various realities we’ve seen, the Molecule Man is always the same. He was likely created by the Beyonders to act as this bomb.
The Beyonders may be all-powerful, but they have one weakness. They exist outside of multiversal space (and therefore will not be undone by their own plans), but they are “glued” to linear time (i.e., they cannot time travel). Dr. Doom was able to exploit this weakness since he can easily travel through both time and space. He started murdering the Molecule Men in every universe to prevent them from destroying everything. After seven years of this, the incursions began; a side effect of what he was doing. The destruction of the Molecule Men resulted in such a massive release of energy that universes literally began to collide with each other.
Now this plan might seem nuts, and it is, but Doom knew there was no way to actually beat the Beyonders. Everything was going to die no matter what. But as each Earth shattered, he was able to save small fragments of them and turn them into something new.
For a more detailed explanation of all of this, see New Avengers #33. The important takeaways from this are: Doom has figured out a way to salvage some of what was destroyed in the incursions, and Dr. Strange is working with him because he believes Doom is right and this is the only way.
Pages 6-8
Here we are at the beginning of the final incursion: the collision of Earth-616 and Earth-1610. Earth-616 is the main Marvel Universe, the one that has been written about since the birth of Captain America during World War II. Earth-1610 is the Ultimate universe, written about since around the turn of the century.
So this is the Ultimate universe that we’re seeing, *not* the main Marvel Universe. Reed Richards-1610 has convinced Nick Fury-1610 that they might be able to prevent the destruction of their planet if they destroy Earth-616, but he knows they’re actually out of time. He has another plan, one that involves the Cabal.
The Cabal are from 616, and they’re like an evil version of the Illuminati. Eventually, the Illuminati came to believe that what they were doing was wrong; that they could not kill other Earths to save their own. Namor disagreed, and freed several big nasties like Thanos, Terrax and the Black Swan to help him kill these other Earths during incursion events. When the Illuminati learned what he was doing, they trapped the Cabal on a dying Earth, hoping to destroy them all. Instead, the Cabal ended up on Earth-1610 with Reed-1610. Their plans are still a mystery.
Pages 11-20
Not much to explain here. This is the battle between Earth-1610 and Earth-616. Earth-1610 loses…or so it seems!
Pages 21-24
Reed-1610 launches a second wave, and here things start to go badly for Earth-616. Lots of heroes die in this attack. Of course, it’s all a cover for Reed-1610 to launch a ship patterned after the ship Reed-616 is trying to launch.
Something that’s important to note about the machine they have Eden (aka Manifold) strapped into: Manifold’s powers are based off of need. He pictures where he or others need to be, and he is able to teleport them there. This machine will allow him to expand his powers across the entire planet, and to reverse them; he’ll be able to bring the “needed” heroes onto the liferaft.
These liferaft ships have been built to withstand the destruction of their respective Earths. They can exist between multiversal space just like the Beyonders. The 616 ship is loaded with the Fantastic Four family and Black Panther. The 1610 ship contains Reed-1610, the Cabal, and a stowaway (as seen on page 21).
Page 25-29
Nobody knows how or why Cyclops has a Phoenix egg, but he is able to use it since he was the last host of the Phoenix force (in Avengers vs. X-Men).
Spider-Man, Thor, Star-Lord, and Captain Marvel are the characters pulled into the 616 liferaft by Manifold, but nobody knows yet why these particular characters are “needed.” It’s also unknown if Phoenix/Cyclops was pulled in by Manifold or if he pulled himself onto the ship.
Page 30+
The final incursion. Much sadness. Not much to explain here.
Next, read Secret Wars #2. This is the introduction to Battleworld, the realm Doom and Strange have managed to cobble together from all of the destroyed Earths.
And now! Now you can get into the really fun stuff. There are a bunch of different series set within these different realms…and everything is weird in each one in different ways, so you’re really not even *supposed* to know what’s going on. For you, I recommend the following books: