So Nathaniel Adams was sentenced to death, but made a deal with the military that he would subject himself to a military experiment and he would be released if he survives. While the experiment is commencing, Adams is trying to calm himself by cracking jokes.

Adams is being subjected to an unidentified metal alloy from an alien spacecraft which the military believes (after trying to break through) could protect a man on the battlefield better than anything. As the alloy is attuning to Adams, he breaks free of the chamber and not only flies, but accidentally shoots down an aircraft!

After being gunned down by soldiers, the alloy becomes dormant and starts to compress itself into Adams, seeming more form-fitted to the human host. And as it turns out... It’s waking up YEARS LATER. (18 years later)

General Eiling who controlled the project began to explain how long it’s been to Captain Atom, and upon the news of telling him about the death of his wife, Adams lashes out and is then immobilized. Eiling states the being is alien and violent.

Eilings speaks with Dr. Megala, who was the originator of the project. Megala explains the reasoning of Captain Atom being gone for 18 years is because he somehow jumped through space-time, and that this could be a giant step for the U.S. military. As Eiling leaves, he orders a hit on Dr. Megala. Eiling then has Captain Adam captured and brought aboard a spacecraft.

Adams wakes up as he leaves earths atmosphere and destroys the spaceship, falling back down to earth. After discovering he can fly, he makes his way back to what would have been his house if it was still 1968 and not 1986. He’s met by Dr. Megala who survived his assassinated. Dr. Megala then begins to help Adams understand his new quantum powers and control them.

After mastering his abilities, Adams is now also able to control his appearance. General Eiling and soldiers make their move on Megala’s mountain home, but are no match for Captain Atom.

General Eiling shows Adams where his wife is. She’s buried at a cemetery... with the last name “Eiling.” Apparently after three years of mourning, she married General Eiling, and the children of Nathaniel Adams became General Eiling’s step-kids.

With his original pardon-agreement null-and-void, Eiling gives Adams a new pardon in which he uses his newfound quantum powers for the U.S. government as part of Phase Two: Captain Atom.