The Beyonder is finally determined to destroy all of existence, including his own memory of it, a prospect which appears to make him feel uncomfortable.
Volcana calls the Avangers hotline to warn them about the Beyonder's plans. However, she ends up speaking to the Fantastic Four, and warns them of what happened at her apartment.
Suddenly, and to their great surprise, most of Earth's heroes are transported to Colorado. Phoenix appears before them all to discuss the Beyonder's plans, and how to save the Earth. Volcana offers to help too, but the other heroes dismiss her as being inexperienced and send her back home. There she enters her apartment to find it has been thoroughly destroyed. She cried out when she finds the Molecule Man slumped in a chair.
No longer able to interest himself in the world, even in "nifty gadgets" like his helicopter, the Beyonder creates an underground lair. He films himself as he recalls the events and tensions of his time on Earth. When he came, he encountered desire for the first time, brought about by people's incompleteness. But as an essentially infinite being himself, he has never ben able to come to terms with this situation. And so he desires to once again be complete, by destroying everything, including his own memory. But, he doesn't remember anything from the period before he looked through the pinhole and saw our universe for the first time. If he erases the universe and his own memory, will he have a mind any more? Will he, in effect, be erasing his self along with everything else?
Instead, perhaps he should try to experience the risk of ordinary mortal death? Therefore he decides he to become mortal, and be born again. But instead of relying on a human woman with a gestation period of 9 months, he creates a "Mama" machine. To test the machine he collects the wisps of energy that used to be the New Mutants (see New Mutants #37) and throws them into the machine. One by one the New Mutants are spat out by the machine, each one dressed and at the age they were before they were killed, but with no memories or minds. He considers this a success, and decides to take his turn. He stores his power in a special container, then streams his self into the machine, where he is transformed into a fetus, a baby, and then eventually a grown man. The sensation freaks him out, and he reaches back into the container to regain his cosmic powers.
Back in Denver, Molecule Man wakes up. He had been distraught when Volcana left him (Secret Wars II #8), but in their time apart he grew to understand that he could survive without her. Knowing now that he can rely on his own sense of individual self-worth, he realizes that he is even better suited to be in a relationship with her. They make up, confessing that they love each other all the more. However, Molecule Man is now determined to stop the Beyonder once and for all. The rest of the cosmic entities are afraid, and it is up to him.
Meanwhile, the Beyonder once again enters the Mama machine, and this time he is excited at the experience of being in his mortal form. However, Mephisto and a horde of demons seize the chance and attack. He begins to torture the Beyonder, who eventually is able to seize the clarity of mind to realize that Mephisto is incapable of incurring real injury on the earthly plane, and that all this is an illusion. He runs to regain his power, but is stopped by yet another illusion. When he reaches toward the container, it seems as if his arm is burning. He summons up his willpower, however, and manages to push through, regaining his power. He doesn't know what to do--he is obviously too vulnerable in an all-human form.
On the surface above the Beyonder's home, the heroes prepare to attack. Molecule Man and Volcana appear, and are ready to lead the way. The Beyonder is aware of their presence, and therefore programs the New Mutants to fight the heroes so that he can reprogram the Mama machine once again. He resurrects Warlock to complete the team and teleports them to the surface. As the New Mutants had been erased from history, none of the heroes recognize them, and think they are just kids. While the Avengers, Fantastic Four, X-Men ad Alpha Flight try to pull their punches on the kids, The New Mutants fight ferociously, and they successfully manage to slow the heroes down. However, they are outnumbered and eventually defeated. Phoenix uses her telepathic powers to read their minds, and learns about how the Beyonder had killed and resurrected them so callously.
The heroes drill down to the Beyonder's underground lair, using the Molecule Man's powers. Unhappy that he must once again fight them, he knocks them all down with one gesture. Even powerful heroes like the Silver Surfer, Rachel Summers, and Thor are knocked down like rag dolls. The only one left standing is the Molecule Man. The two "mightiest beings in all existence clash, and every creature on every planet in every dimension feels the multiversal tremors born of their fury." The Molecule Man stands toe to toe with him for a short time, but is overpowered and not used to battles. The other heroes get up and attack again. The Molecule Man is canceling out the Beyonder's powers to the extent that the others are almost able to affect him--the Beyonder admits they actually had a chance--but then he knocks them all aside again, this time including the Molecule Man along with the rest. He shoots a massive bolt of energy down at them from space, rending the crust of the planet and blasting all the heroes away.
Now that he is abe to concentrate, the Beyonder throws his energies into the Mama machine once more. While he is in the gestation cycle, the heroes slowly get back to their feet, a far distance away. It turns out that the Molecule Man had created a shield large enough to protect them all, while also putting every other living thing into stasis in subspace. This effort, however, left Reece badly hurt. Phoenix teleported the heroes back to the Beyonder's lair, where they prepared another attack, but they soon realized that he was now just a baby in the Mama machine. Some of the heroes were still willing to kill it, but others held back, feeling that killing any baby would be an atrocity.
While they argued over the ethics of killing a baby, the machine's defence systems created an explosion equivalent to a nuclear bomb. They were saved only by Susan Storm's forcefield, which was strengthened by Rachel Summers and the Silver Surfer. Storm passed out from the effort, and the heroes were now spurred to attack no matter what. However, Mr. Fantastic stopped them, reasoning that the machine didn't just contain a human infant, but the Beyonder's cosmic powers as well, and so if the baby was killed, it might release all those powers in a destructive explosion. Owen was not convinved. Volcana implored the Molecule Man not to harm a baby, but ultimately he knew that it was the only way to save the Earth. Molecule Man blasted the Mama machine. The baby died, and an explosion flooded the world in a blinding white light, just as Richards had predicted. However, the light receded, and we see the Molecule Man sending the Beyonder's energy through an interdimensional portal.
The Silver Surfer carries the lifeless body of a baby out of the broken Mama machine, and the heroes walk away, saddened. Volcana comforts Owen, and Captain America thanks him for saving them all. They acknowledge that it was not an ideal solution, but admit that it did save the Earth. Owen says that it is a happier end than Captain American knows.
Elsewhere a portal opens. The white nothingness of the empty Beyond-realm rapidly fills with the Beyonder's power, just as with our own universe's Big Bang. The power eventually cools and creates a new universe, complete with stars, planets, and evolving landscapes. Evolution occurs as on earth, from fish to amphibians, and eventually to apes and even humans. "Thus, within the new universe begat by the Beyonder's power...moral beings live their finite lives...giving meaning to the infinity in which they dwell...Thus, finally, is the desire of the one from Beyond...fulfilled!"
The story is concluded in an epilog in Avengers 266.