With Brialeos convalescing after a mission, Deunan is assigned a new and remarkably familiar partner as a strange wave of terrorist attacks plague Olympus.
When a paramilitary task force called E.S.W.A.T. and its operations in the year 2133 Olympus, a futuristic utopia where humans, cyborgs, and bio-engineered human beings called "Bioroids" are attempting to live in perfect harmony. However, a series of random terrorist attacks perpetrated by cyborgs and humans alike threaten to throw Olympus into total chaos. As it turns out, these humans and machines have come under the influence of an unknown electronic signal that hacks into their nervous systems and they then become the unwilling servants of a malevolent computerized entity. Thrown into the action is the plucky female E.S.W.A.T. warrior Deunan Knute and her cyborg lover/partner Briareos as they investigate these bizarre occurrences with the other members of their unit. Things become complicated when a bioroid named Tereus, who resembles Briareous in his human form, joins their unit and threatens to come between their relationship. But these three must put aside their differences to face an even greater threat that promises world destruction in its wake.—Anthony Pereyra {hypersonic91@yahoo.com}
Following the events of Appleseed, ESWAT members Deunan Knute and Briareos Hecatonchires infiltrate a cathedral somewhere outside of Olympus and find European Union officials taken hostages. After rescuing the EU officials and destroying the cyborgs, ESWAT return to Olympus, where Briareos is confined to hospital until he recovers, while Deunan continues ESWAT work. When Deunan's commanding officer Lance introduces her to her new partner, Tereus, she is shocked as her partner resembles Briareos' human form.
Deunan confronts Lance for an explanation, and is given the tour of the new Bioroid production facility. During the tour, Hitomi, a bioroid that Deunan befriended during those events, is mentioned to now be a minister of political affairs. Here it is shown that Tereus is actually a Bioroid; a prototype for a whole new production line of Bioroids to be soldiers without negative emotions to impact their judgment in fighting. As his physical and mental strength was found to be most desirable in ESWAT, Briareos' DNA was used mostly in Tereus' design. Reluctantly, Deunan is partnered up with Tereus to evaluate his performance. While departing, Deunan encounters Hitomi and Hitomi gives her a ride home. Deunan notices that many Olympus citizens are wearing Connexus; a device on their ears which projects holographic data over the eyes.
Deunan, Lance and Hitomi visit Briareos, still recovering in hospital. Here, Lance states that out of the last five terrorist incidents, four of them have been by groups composed solely of cyborgs, with transmitted signals from surrounding locations, thus suggesting that digitally vulnerable cyborgs are actually being manipulated to perform these acts. Because many of these cyborgs consist of parts made by Poseidon, a multinational industrial conglomerate, an emissary is sent to Prime Minister Athena. The emissary denies Poseidon blame, but Olympus still boycotts them, which Poseidon finds undesirable as other world powers may follow suit.
Meanwhile, Hitomi hosts a birthday party, in which Deunan is happy to find Briareos attending now that he's fully recovered. Briareos meets Tereus for the first time - which makes him uncomfortable - but the two accept each other. Briareos also accepts Deunan's new partnership with Tereus, and has found someone other than Deunan to partner with, which upsets her. She storms off, but is eventually joined by Tereus, who displays many of Briareos' personality traits, which by Deunan's own admission makes her feel "confused."
The next day, Athena and an assemblage of world leaders discuss making a global security network by merging all the satellites worldwide to prevent terrorist attacks before they happen. ESWAT and the Olympus police forces set up barricades around the conference hall. ESWAT personnel pick up the broadcast of an unknown signal. Soon enough, a variety of vehicles and non-cybernetic humans begin to assault the conference, much to the confusion of ESWAT and the regular police. Even more strangely, at the same time, Aeacus kills a engineer on board an ESWAT transport, declaring, "We will all be one. I am Halcon" and destroys it to escape wearing his Land-Mate. Briareos rushes to the explosion, and initially tries to stop Aeacus but ends up killing him. As Deunan and Tereus arrive, Tereus uncovers the mysterious signal coming from robotic doves. Simultaneously, the unknown signal disappears, and the attackers collapse. A funeral is held sometime later for Aeacus.
At the same time all the satellites are joined, Briareos is nearly run down by an unmanned vehicle. He stops it but suddenly goes berserk and hacks into a public terminal, crashing the main satellite control, forcing Olympus to switch to a backup. Briareos is hospitalized, with the unknown signal ruled out as the cause of his outburst. Briareos gets suspicious of his cyborg doctor, Richard Kestner, who operated on him after his accident. He has Hitomi look up Kestner's files, learning that he once worked with Poseidon's Halcon Laboratories - but all records of his project are mysteriously erased. Briaereos breaks out and tracks down Kestner, who confesses that he is part of a plan to "unify" humanity through erasing individuality, to which he attributes the source of human conflict. He then reveals that he secretly injected Briareos with nanites designed to take control of his body when his adrenaline heats up. Kestner then commits suicide before the police arrive, making them think that Briareos killed him. Briareos escapes, but is cornered by Tereus. Deunan arrives just on scene with an antidote designed to suppress the nanites.
The virus Kestner placed in the backup network takes control of the satellites and, through these satellites, all people linked to the Connexus, compelling them to riot against Olympus. Believing that Poseidon knows something about all this, Briareos, Tereus and Deunan track down a Poseidon convoy to learn about Halcon. As they discover, Halcon was once the leading scientific laboratory until they started mind control experiments, which Poseidon was forced to end when the project lead Elizabeth Xander was killed in an accident. Poseidon assists the ESWAT officers in infiltrating the fortress where the Halcon signal is transmitting. Once they are in the control center, they discover that Xander was resurrected as a cyborg to control all those linked to the Connexus. After destroying her, thus freeing all the enthralled, the heroes escape the collapsing fortress and return to Olympus.
