Issue 1‘s events follow on directly from Countdown To Infinite Crisis with Max Lord, now head of the Checkmate organisation, having killed Blue Beetle and ordering Sasha Bordeaux to “clean it up” and remove Beetle’s body.
Querying the Brother Eye database, Lord finds that all files collected on the various metahumans, both hero and villain, have been deleted and assumes Beetle removed them. Brother Eye itself, however, claims that it was its creator, Batman, that removed them, prompting Lord to begin surveillance of Batman and other associates of Beetle.
Batman, meanwhile, attempts to communicate with Brother Eye only to find himself locked out of the system.
Booster Gold, Beetle’s long time friend, is contacted by Wonder Woman. Of all the people Beetle told of his suspicions in Countdown, she was the only one to have believed him and, with Booster, begins searching for him.
Knowing that the murder of Blue Beetle needs to be addressed, Bordeaux manages to get his goggles and a warning to Batman.
Issue 2 begins with Batman explaining to Superman, Wonder Woman and Booster Gold why he created Brother Eye as a surveillance system to watch the metahumans of the world: the mind-wiping performed upon him by the Justice League and shown in Identity Crisis left him feeling betrayed and determined that it should never happen again to anyone. He reveals Beetle’s goggles, concluding that he has been murdered.
Displaying his level of control, Lord watches the discussion on a monitor, clearly illustrating he is able to see even into the JLA Watchtower on the moon. Seeing Beetle’s goggles makes him realise there is a traitor in Checkmate.
The Russian criminal Overthrow is killed by an OMAC, one of millions of normal humans that Lord has infected and given the ability to transform into a lethal automaton.
Lord calls a council of Checkmate, inviting the other leaders, along with Bordeaux, to meet with him. Correctly anticipating an assassination attempt, Lord pre-empts them and, using his mind controlling ability, forces her to kill the other royals of Checkmate. She is then sent to Chicago to ensure that Blue Beetle left no clues to Checkmate behind. There she is met by her ex-lover, Batman, with Lord watching all the while. With some regret, Lord orders three OMACs to attack them.
Issue 3 The attack by the OMACs on Batman and Sasha reveals that Batman had no hand in their creation. Watching all the while, Lord alters the OMACs commands to capturing Bordeaux and killing Batman. Two of the three OMACs escape with Bordeaux leaving the final one to eliminate Batman; it is prevented in this, however, by the arrival of Superman.
Booster Gold and Wonder Woman, meanwhile, search Earth’s orbit for any sign of the Brother Eye satellite but find nothing. They are joined by GL Guy Gardner whose rude manner infuriates Wonder Woman to the point where Booster is forced to ntervene in their bickering. While he appreciates her help, Booster informs her that he should take up Gardner’s idea to reunite the members of their incarnation of the Justice League to look for Beetle.
Lord questions the captive Bordeaux, trying to find out how much Batman knows of the OMAC virus, the infection that allows him to choose which of the general public becomes an OMAC. However, for some reason, Bordeaux is immune to his mind controlling abilities.
At the JLA Watchtower, Batman, Superman and Wonder Woman discuss what to do with Batman determined to find out who controls Brother Eye and shut them down. Superman and Wonder Woman both head back to Earth.
Lord, feeling his hand is forced, contacts Superman in his alter ego of Clark Kent and, over a video link, uses his ability to control minds to convince him that his enemies are out to harm both Superman himself and those he loves. This leads directly into the Sacrifice storyline.
Issue 4 starts with Brother Eye recapping the events of part 4 of Sacrifice, namely the attack by a controlled Superman against Wonder Woman as she holds Max Lord captive. Lord is heard to say “Kill me.” and may well have been using his mind control to force Wonder Woman to do just that; with a twist of her hands, she breaks Lord’s neck. With its controller dead, Brother Eye becomes intent on surviving and causes numerous distractions around the world, forcing Superman and Wonder Woman to leave the castle to face them.
Brother Eye engages its Scorched Earth protocol and sets about killing the remaining personnel of Checkmate, part of which includes starting the process of turning Bordeaux into Black Knight One, an improved version of the OMACs.
Booster Gold and GL Gardner find their old Justice League teammate Fire already investigating the disappearance of Blue Beetle and stuns Booster by asking if Beetle had any contact with Lord before he went missing (this was shown in Countdown To Infinite Crisis).
Brother Eye contacts a recuperating Batman in his Batcave and relays footage of Rocket Red and the Martian Manhunter battling an OMAC in Russia as well as Bordeaux being attacked and apparently killed by another OMAC in the castle.
Issue 5 Cutting off the video feeds to Batman, Brother Eye leaves him under the impression that both Bordeaux and Rocket Red have been killed. However, the battle between Rocket Red, Martian Manhunter and the OMAC is interrupted by the arrival of Booster Gold, GL Gardner, Fire and their new recruits, Metamorpho and Mary Marvel. As an aside, Mary Marvel was only affiliated with Booster’s incarnation of the League in the mini-series “Formerly Known As The Justice League” and its follow-up in the JLA Classified storyline, “I Can’t Believe It’s Not The Justice League”. As a result of Infinite Crisis, it appears these storylines are no longer in continuity.
As the battle rages, Brother Eye begins a countdown to total OMAC conversion – a process which will mean the satellite itself has to go off line.
Reinforcements for the OMAC arrive and systematically take out the collected heroes until Rocket Red, in an act of self sacrifice, causes his suit to explode, killing himself and the three OMACs.
At the Checkmate castle, Bordeaux is revealed to have survived by becoming Black Knight One, essentially an autonomous OMAC v2. She contacts Batman to warn him that Brother Eye is turning on all of the OMACs, all 1,373,462 of them.
Issue 6 As the entire OMAC population is activated across the world, with many of them going into Earth orbit to protect Brother Eye, Bordeaux contacs the other government agencies such as the DEO, STAR Labs and the Freedom Fighters, and coordinates their resistance tactics.
Batman meets GLs Hal Jordan and John Stewart in the Kord warehouse that was burgled back in Countdown To Infinite Crisis and charges them with the task of baiting the OMACs into a trap using a mas Electromagnetic Pulse generator. It was this generator that was the original focus of the burglary as Lord knew it would be a threat to the OMACs. As it had not been delivered at the time they broke in, however, the OMACs took the Kryptonite to cover their tracks.
Booster, GL Gardner and Fire meet in the hostpital where Fire is being treated following the battle with the OMACs; as Gardner goes to join Jordan and Stewart, Booster leaves the hostpital saying he’s “going back home.” It’s revealed in Infinite Crisis #1 that Booster had returned to the 25th Century after leaving the hospital.
The Green Lanterns gather as many heroes as they can, following Batman’s plan, and draw the OMACs to them; during the battle, Batman flies in and delivers the EMP generator, knocking out the OMACs, leaving around two hundred thousand around the world and guarding the Brother Eye satellite.
While defeated, however, Brother Eye is still able to strike and broadcasts to screens around the world the image of Wonder Woman killing Max Lord which leads into Infinite Crisis #1.
The OMAC Project Special takes place directly after Infinite Crisis #6. In that issue, Batman and a collection of heroes caused the Brother Eye satellite to fall from Earth orbit; here it crashes in the Saudi Arabian desert and instantly becomes the focus for several nations’ attempts to capture it.
Amanda Waller is appointed acting head of Checkmate by President Horne and charged with finding the satellite, using Checkmate’s remaining facilities along with the presence of Fire.
While the Russians, Israelis and Chinese all battle the last surviving OMAC that guards the satellite, Bordeaux in her guise of Black Knight One, manages to gain entrance to the satellite carrying a satchel of explosives.
She detonates the bomb, destroying Brother Eye and, in turn, killing off the nanobots that had turned her into Black Knight One leaving her relatively unharmed and, as far as we are aware, more or less human again.