Issue Armageddon: The Alien Agenda 1
Subtitle Days of Thunder Lizards
Date November 1991
Writer(s) Jonathan Peterson
Artist(s) Dan Jurgens, Steve Leialoha
storyline Captain Atom stood atop a hill and watched dinosaurs in their natural element. A T-rex attacked and almost ate him. After chasing him off, he realized he wasn't at full strength. Monarch watched. A ship of aliens nearby noticed the two new intelligent life forms on the planet.
The alien ship landed. Atom and Monarch were brought aboard. They said they, too, were traveling through time and space and could possibly help each other.
That night, the aliens told Monarch they had a common enemy - Captain Atom.
Atom overheard some of the aliens discussing their plot to pull all the planets in the system together to create a wormhole. He grabbed their detonator and used it on their ship. After the explosion, he found himself naked on his back looking up at what appeared to be ancient Roman soldiers.

Issue Armageddon: The Alien Agenda 2
Subtitle Rome Alone
Date December 1991
Writer(s) Jonathan Peterson
Artist(s) Mike Netzer, Joe Rubinstein
storyline The alien ship - with Monarch - returned to orbit and docked with the mother ship. They were convinced Captain Atom was a scout sent by their enemies. The planned to place Monarch in a suspended animation chamber coded to their detonator. When the time was right and the two devices crossed paths, Monarch would be freed to find Captain Atom and retrieve the detonator. He would then activate another device to return to the aliens' time.
Captain Atom, who'd lost his metallic skin and was hardly able to touch the quantum field, was captured by Roman soldiers and taken to Emperor Nero. They took him as a demon - he had a Christian symbol (the marking on his chest) and a sorcery device (the detonator). He was thrown into the gladiator arena to fight lions.
Elsewhere on the planet, the aliens (who'd been behind their city walls for eons), greeted one of their time displaced soldiers. When he awakened, the people (generations down from those who actually landed) thought he was a statue come alive.
Captain Atom was able to access enough of his power to defeat the lions thrown at him. He was taken in by the emperor.
The alien warrior teleported to the detonator. Captain Atom regained his armor in time to be attacked by the alien. He crushed the detonator, once again displacing him in time.

Issue Armageddon: The Alien Agenda 3
Subtitle The West Years of our Lives
Date January 1992
Writer(s) Jonathan Peterson
Artist(s) Alan Weiss, Joe Rubinstein
storyline Captain Atom found himself in the middle of a stampede in the American Old West. He was rescued by some cowboys (including Matt Savage and Johnny Thunder). Once he recovered, the three headed into town to find the detonator - one of the other men had found it and taken it to trade. Once in town, they got into a huge bar fight (featuring Bat Lash, the Trigger Twins, Jonah Hex, Pow-wow Smith, Bull Honee, etc.).
Monarch and the rest of the soldiers awoke from suspended animation (still in ancient Roman times). A rebellion broke out against Prime One (the leader) and he was killed by military forces.
Somehow, during the bar fight, Monarch attacked Captain Atom - he had the detonator. One of the aliens was there, too. A blast from Monarch's energy rifle set off an earthquake. The earthquake set off the detonator, and Captain Atom found himself in Nazi Germany.

Issue Armageddon: The Alien Agenda 4
Subtitle All this, and World War Too
Date February 1992
Writer(s) Jonathan Peterson
Artist(s) Dick Giordano, Steve Mitchell
storyline Captain Atom was beaten by the Nazis and thrown in with other prisoners. Monarch was also in WWII times - he stumbled upon some Japanese soldiers.
After seeing what captivity was doing to some children, Captain Atom mustered enough energy to suit up. He blasted through the walls and attacked Nazi soldiers. He freed the captives and obliterated the camp before flying off with the detonator.
Atom flew to Japan where he knew the US would be testing an atomic bomb. There, he found Monarch. They fought once more. The detonator cracked open sending them through the time stream again.
Captain Atom made it home. Meanwhile, in an underground alien city, the monitor activated - Captain Atom was near.

Notes, references to time, and chronology:
  This is a direct continuation of the Captain Atom / Monarch storyline from Armageddon 2001.

   
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