The War Begins
The story begins when a team of heroes finds themselves transported to a space station in an unknown region of the galaxy. The heroes' team is comprised of Captain Marvel, Captain America, Wasp, She-Hulk, Thor, Hawkeye, Iron Man, Professor X, Storm, Nightcrawler, Rogue, Cyclops, Wolverine, Colossus, Lockheed, Spider-Man, Mr. Fantastic, Thing, Human Torch and Magneto. The heroes quickly realize that they are not alone as a second space station hangs not far away, in perfect view from theirs. This is where a similar group of villains has been transported, consisting of Enchantress, Ultron, Absorbing Man, Wrecker, Thunderball, Piledriver, Bulldozer, Kang, Galactus, Lizard, Molecule Man, Doctor Octopus and Doctor Doom.
The two groups are made aware of each others' presence and transported to a planet made up of pieces of other planets by the Beyonder. While the location of this planet is not known exactly, Doctor Doom believes that it is in orbit of a star that is the last star of the galaxy that they are in. There is immediate turmoil among the villains as they begin to fight with one another. Ultron makes a first strike against Galactus and is drained of all his energy for his trouble. The Beyonder then tells them to fight and that the victorious group shall be granted all that they desire. Galactus and Doctor Doom immediately attempt an attack on the Beyonder in an attempt to seize his power for their own, but they are swatted away like flies. The heroes are in awe, having witnessed this display of power and realizing how easily he defeated two of their greatest enemies.
The two groups are then transported to the planet surface with the exception of Galactus and Doctor Doom who land there after being knocked back by the Beyonder. The heroes immediately attempt to attack Magneto, but rather than fight, he repels himself into the sky by riding the magnetic waves of the planet. Doctor Doom finds a fortress and hopes to rally the villains to stand against the Beyonder, but they rebel against his plan and so he sets out to obtain the Beyonder's power for his own. Kang witnesses Doctor Doom attempt to leave and uses weaponry available in the fortress to blast Doctor Doom out of the sky. Doom conveniently crashes near the heroes, followed shortly by the group of angered villains and the first battle of the series ensues.
Prisoners of War
As his allies do battle with the heroes, Doom attempts to take council with Galactus, but is ignored. He then goes back to the fortress to see what kind of technology has been provided for the Beyonder's victims to use in the war game. He makes quick work of the fortress' defense systems and discovers an inert Ultron
. Meanwhile, the heroes defeat several of the villains, and the remnants flee from the battle. In need of a place to detain the captured villains, the heroes discover that a fortress has been provided for them as well. Rather than press their advantage, they decide to regroup and prepare for a long series of battles by learning about their new, temporary headquarters. Magneto finds yet a third fortress, located hundreds of miles away from the other two and plans his next move as well.
The villains return to their fortress only to be assaulted by Doctor Doom and a rebuilt Ultron that now serves him. Under their combined might, the remaining villains are subjugated and agree to obey Doom's leadership. Meanwhile, the heroes attack Magneto at yet the power plant and Wasp is captured by Magneto during his retreat. During the confrontation, Thing discovers that he is able to revert to his human form.
Tempest Without, Crisis Within
Magneto takes Wasp back to his fortress and the two are trapped there as the weather in his section of the world changes and prevents them from leaving. Spider-Man overhears Charles Xavier (now able to walk) and the X-Men planning to leave the heroes and join with Magneto and attempts to intervene and stop them. Spider-Man attempts to report the activities of the X-Men to the Avengers, but has his memory altered by Xavier before he can do so.
Doctor Doom suggests an alliance with Magneto, but is turned down. Magneto then returns to Wasp and the two share a moment while the storm rages outside. At Doombase, Doctor Doom begins experimenting on Skeeter (who was not previously mentioned in the series) and grants her new powers. With her new powers, she chooses a new name and becomes Titania. The second subject that Doom experiments on is granted the power to project plasma and chooses the name Volcana.
Thor frees Enchantress and the two depart to have a moment away from the mortals. At dawn, Doom leads an assault against the heroes' base with the remaining villains and manages to catch the heroes off guard. Using their advantage, they force the heroes to regroup while the prisoners are freed. The heroes' base is destroyed but the villains discover that the heroes managed to escape while checking the wreckage.
The villains quickly spot the fleeing group and use their combined might to throw a mountain on the heroes. Thor and Enchantress are interrupted by the concussion of the falling mountain and return to the ruins of the heroes' base only to appear in the middle of the villains. Thor takes on the villains single-handedly but is defeated and vanishes, leaving only his helmet. Doom then orders Ultron to kill Kang for his earlier attempt to take Doom's life.
The X-Men arrive at Magneto's stronghold and form an alliance with their former enemy. Magneto then reveals that he believes the heroes should take an aggressive role and do as the Beyonder requests: kill the villains and claim the prize. Wasp then compares him to Hitler and flees from the base. Meanwhile, the heroes are revealed to have survived the mountain toss, as Hulk caught it on his back and prevented it from crushing the group. Iron Man's armour was damaged, and with Hulk only able to hold the mountain up, they are effectively trapped. Mr. Fantastic then uses Hawkeye's arrows and Spider-Man's web shooters to repair Iron Man's armour and he blasts an escape path through the mountain. As they exit, Thor returns to the group, explaining that he hid his escape with a flash of lightning. The heroes then regroup to a village that was brought to the planet, but are concerned with Galactus who is standing on top of a nearby mountain.
The Battle of the Four Armies
Galactus then moves, and summons his ship to the planet. Seeing the ship in the sky, Magneto and the X-Men leap begin making their way to Galactus. Also seeing the ship, Doom begins preparing the villains for battle as well. Charles Xavier and Magneto attempt a combined psychic attack on Galactus while Mr. Fantastic attempts to distract him. Galactus unleashes a robot from his ship to fight Captain America's faction while repelling the psychic attack. The America faction defeats the robot, but not without leaving several members of the team incapacitated. It is then that the Doom faction steps in and attacks the heroes. The heroes are hard pressed, and in danger of being defeated when Magneto and the X-Men arrive. While Galactus is distracted by the battle at his feet, Doom sneaks on board Galactus' ship. Eventually the Doom faction is driven back, but Colossus is gravely wounded. Magneto and the X-Men depart, leaving Colossus behind (not without protest of several of the X-Men). Galactus continues to construct his world devouring machine, unhindered.
A Little Death...
Wasp begins making her way back to the America faction. Doom, exploring Galactus' ship, discovers Klaw, the self-styled master of sound. With new orders from Doom, Klaw returns to the villains. Xavier takes a moment to rest his legs while the X-Men survey the damage done to their base by Galactus' psychic attack. While resting, Xavier stretches out with his mind and touches the minds of the villains, ascertaining their new plan. He then orders the X-Men into action. Storm, unhappy with Xavier's new direct leadership role, confronts him. Xavier then tells her that he would go so far as to alter the memories of the X-Men to prevent insubordination. Meanwhile, Colossus begins to show interest in an alien woman named Zsaji but she is whisked away by the Human Torch. The villains arrive at a volcano and begin setting Doom's plan into motion but are attacked by the remaining X-Men. During the fight Molecule Man is seriously injured by Wolverine and the villains flee. Cyclops, realizing that their plan was most likely to harm Galactus, fires his optic beam into a region of volcanoes, igniting them. In an unexpected turn, Wasp is then shot and killed by Wrecker as the villains make their way back to Doombase.
Spider-Woman joins Captain America's faction, having been uprooted from earth during the construction of the planet. The Wrecking Crew tosses Wasp's body into the village as they continue towards Doombase. Zsaji, the healer, attempts to help Wasp but it is too late. While the Avengers try to decide their next course of action, the X-Men continue to pursue the fleeing villains.