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Flashpoint was a five-issue mini-series centered around the Flash and leading into the New 52.  The plot was beautiful in it’s simplicity and a pretty good read, if you overlook the abundance of convenient coincidences.  Basically, the Flash learned that Professor Zoom (Reverse Flash) was the man who murdered his mother.  So Flash used his speed powers to travel back in time to save her.  This action screwed up the time stream in such a cataclysmic way that he himself no longer had superspeed, Bruce Wayne was gunned down as a child and his father became the Batman, and Wonder Woman and Aquaman were having a war to end all wars.  And Superman’s rocket didn’t crash in Smallville but in the heart of Metropolis, where the baby Kryptonian was kept a prisoner his entire life.  Pretty crazy stuff.

The mini-series was written by Geoff Johns with art by Andy Kubert.  There were several tie-in series in 2011 that expanded the new universe the Flash had inadvertently created.  Just about every major character in the DC Universe was altered in some way, and Captain Atom was no exception.

Nathaniel Adam is first seen in Flashpoint: Frankenstein and the Creatures of the Unknown #1 (written by Jeff Lemire, pencils and inks by Ibraim Roberson, colors by Pete Pantazis, and letters by Pat Brosseau).  After being frozen for 60+ years, Frankenstein and his creature pals awaken in the same military/science complex that was holding Superman.  Upon their escape, the director of the facility is introduced.  It seems Nathaniel Adam was never accused of murder, never signed up for the Captain Atom project, and never got a quantum boost into the future.  Now he’s a hardened military man somewhat reminiscent of General Eiling.

We next see General Adam in Flashpoint: Project Superman #1 (written by Scott Snyder and Lowell Francis, pencils and inks by Gene Ha, colors by Art Lyon, and letters by Rob Leigh).  Nate now appears as an ineffectual failure, more doughy and less stern, even though his appearance in the issue was thirty years ago (maybe he has that Benjamin Button disease).

General Adam then appears in Booster Gold #45 (written and drawn by Dan Jurgens with inks by Norm Rapmund, colors by Hi-Fi Design, and letters by Carlos M. Mangual), where he’s controlling Doomsday from a remote location.  This freaks the dimension-hopping time-traveling Booster out because he remembers who Nate was in the “original” universe.

Booster manages to give Doomsday/General Adam the slip, leading Adam’s cohorts to be a little miffed.
Booster hacks into a stranger’s desktop computer and learns the horrible truth about this world.  He learns Batman is operating in Gotham City (or at least, “a” Batman) and heads that way.  Nate’s crew manages to track him down.  They believe Booster to be a terrorist in cahoots with Aquaman.
General Adam’s team manages to get the jump on him just outside Wayne Manor.
A young woman with powers of her own (whom Booster met earlier in this issue) attacks Adam’s mobile command center, causing his link with Doomsday to be broken.
This is pretty bad news for Booster Gold.  Doomsday was, after all, powerful enough to actually kill Superman.
So we are left with that little cliffhanger for 30 days as General Adam next appears in Flashpoint: Project Superman #2 (with the same creative team as issue #1).  It takes place twenty years in the past and tells the story of Sam Lane’s inability to maintain control over young Kal-El.  General Adam pops up at the end and is once again an evil bastard.
General Adam next pops up in Booster Gold #46, continuing his head-butting with Booster (Ig Guara helped with pencils on this one and Ruy José aided with inks).
So Doomsday is no longer under Adam’s control and the General’s command plane is going down.  Booster tries his best against Doomsday but his attacks have little effect.  As the creature uses the hero as a punching bag, Adam’s team regains control of their plane.
Of course, Adam’s assumption that Doomsday is mindless is completely wrong.  He learns the truth once the link with the helmet is reestablished.
Booster takes advantage of Doomsday’s disoriented state and hits the beast with everything he’s got.  In a moment when Doomsday is distracted, Booster slaps the psi-helmet back on his head.
However, this does not exactly mean success for Booster Gold, as General Adam has a serious desire to kill him.  This issue leads into Booster Gold #47, and General Nathaniel Adam’s final appearance in the DC Universe (for now).
This issue was written by Dan Jurgens with pencils by Rick Leonardi and Dan Jurgens, inks by Don Ho and Norm Rapmund, colors by Hi-Fi Design, and letters by Dave Sharpe.  
Booster’s friend Alexandra (a meta-human with the ability to mimic others’ powers – a woman Booster met when he began tangling with Doomsday) pleads with the General, telling him that Gold’s story of time-travel and alternate realities is true.  Adam doesn’t buy it, however, and threatens to use a powerful truth drug on the bound hero.
Booster catches a glimpse of Superman on a monitor, but so does Doomsday.  Doomsday was originally drawn to Superman and killed him.  Booster warns Adam and his team that it is about to happen again.  Before Adam can get the psi helmet back on, Doomsday becomes alert and begins to wail on Booster Gold.  Alex manages to slip the helmet on herself, stopping the monster in his tracks.  Now under her control, Doomsday reaches into his own chest and kills himself.
With Doomsday defeated, Booster and Alex go on to Europe to catch up with the Flash.  General Adam’s part of this story is over.  When the universe was reset after Flashpoint, Nate became the New 52 Captain Atom and this version of Nathaniel Adam never existed.  Well, maybe he is somewhere in the multiverse.  But I doubt we’ll ever see General Nathaniel Adam again.