It is one of four miniseries leading up to DC Comics' Infinite Crisis event. The series directly follows the Countdown to Infinite Crisis special, picking up the story where the special left off. While the OMACs look similar to the earlier Jack Kirby creation OMAC, they are quite different, with a different acronym than the original One-Man Army Corps. OMAC originally stood for Observational Meta-human Activity Construct, but currently stands for "Omni Mind And Community."
In the mini-series, the OMACs are modified humans who work as sleeper agents, a product of the Checkmate organization, now led by Maxwell Lord. They possess the Brother Eye spy satellite built by Batman following his realization, after the events of Identity Crisis, that his fellow Justice Leaguers had wiped his memory some years before. The OMAC Project ends with an autonomous Brother Eye having command of over 200,000 OMACs and seemingly planning war on the superheroes, starting with the worldwide broadcast of Maxwell Lord's death at the hands of Wonder Woman. The OMAC Project has numerous tie-ins with other titles, including Action Comics #829; Adventures of Superman #641-643; Aquaman #35; Batgirl #66; Birds of Prey #80 and 82-83; Firestorm #18; JLA #122; JSA #76; Hawkman #46; Manhunter #13-14; Robin #143-144; Superman #214-215, 217-220, and 222; and Wonder Woman #218-221.
Interwoven through this plot are scenes detailing the power struggle within the Checkmate organization itself. Checkmate is led by the White Queen, White King, Black Queen and Black King, each of whom have Knights of corresponding color. Through his machinations, Black King Maxwell Lord becomes the only leader of the organization, despite being double-crossed by one of his own Knights, Sasha Bordeaux.
Lord is then killed by Wonder Woman (in the pages of Wonder Woman #219) to prevent him from continuing to direct the actions of a mind-controlled Superman. Brother Eye, the artificial intelligence directing the OMAC drones, initiates a protocol specifically designed to be used in the event of Lord's death and OMAC drones worldwide begin to wreak havoc and destruction.
Sasha herself is transformed into an OMAC-like being, powered by nanite technology. Rocket Red #4, a former member of the Justice League Europe, sacrifices himself in order to destroy several drones and save the lives of his friends.
Batman and Sasha then work with the remnants of Checkmate and other government organizations to lure the majority of OMACs to the Sahara Desert. There, as OMACs gather to attack a large number of gathered heroes, Batman activates an EMP device that disables all of the OMACs, allowing their human hosts to be freed. However, the Brother Eye satellite is still hidden and has about 200,000 OMAC's still under its control.
Brother Eye overrides all television screens around the world and broadcasts Wonder Woman's killing of Maxwell Lord. People don't understand the circumstances, only that they're watching Wonder Woman murder a recognized Justice League colleague.
In Wonder Woman #221, Wonder Woman took a defeated OMAC to a hospital, and noticing everyone staring at her in fear, saw the broadcast and realized "They have killed my name."
As the series closes, Brother Eye prepares to launch an all-out war against metahumans to protect humanity. Batman works furiously to disable his rogue creation, while Wonder Woman and the Amazons of Themyscira face international backlash over Diana's brutal means. Brother Eye's campaign against the Amazons leads into Infinite Crisis #1.
Meanwhile, President Jonathan Vincent Horne is being debriefed on the Brother Eye situation by Amanda Waller. Afterwards, he appoints Waller as acting Black King of Checkmate until further notice. In the desert, local forces try to gain control of the downed machinery, but are eliminated by a behemoth OMAC created from the two sentries.
In Switzerland, Jessica Midnight is communicating with Mr. Bones, Director of DEO, when she is quickly interrupted and cut-off by Amanda Waller (flanked by Fire). Waller demands to know what's currently happening, having Fire put the "heat" on Midnight as well as announcing herself as Midnight's new superior.
While the Israeli, Russian and Chinese governments begin measures to retrieve the satellite, Brother Eye attempts to remote link to Sasha and take control of her body. It fails. Sasha arrives at a Checkmate safehouse and attempts to make contact with Midnight at headquarters, but is stopped by Waller, who demands to know if Sasha is an OMAC or not. Sasha does not know. Waller demands Sasha return to base, but Sasha says she will not. Waller then instructs Fire to stop Brother Eye from being reactivated, even if it means killing Sasha or Midnight. When Fire protests such lethal commandments, Waller jabs at her with remarks on what she did for her people in Brazil before gaining her powers, and how much she enjoyed it.
As all of the factions reach the downed satellite, Sasha rushes through the ensuing battle to detonate explosives from within Brother Eye's CPU chamber. The computer nearly succeeds in downloading its programming and data files over Sasha's mind when she activates the explosives. Searching the wreckage, Fire and Midnight find Sasha alive and free of the nanobots that she was infected with.