Set in 1999, Tokyo is undergoing a huge re-development program: old suburbs are being demolished and human-made islands are being constructed in Tokyo Bay under the Babylon Project. Dominating the scene is the Ark, a huge man-made island that serves at the Project's nerve center and chief Labor[b] manufacturing facility. However, several of the Labors being used in Tokyo, specifically those built by Shinohara Heavy Industries, suddenly go haywire even while unattended. The Tokyo Metropolitan Police Department's (TMPD) 2nd Special Vehicles Section (SV2) is assigned to help reel in the errant Labors, but only the SV2's Division II is on duty around the clock (with Division I already on training duties elsewhere). The JGSDF is also preoccupied as they send their own forces to stop an HOS-equipped TYPE-X10[2] Labor tank prototype. As Division II goes out on the field, team commander Captain Gotoh, Sgt Asuma Shinohara, and mechanic Shige Shiba work with police Detective Matsui to find further leads on the case. They discover that all the errant Labors, plus other Labors in the Greater Tokyo Area, were equipped with the company's new Hyper Operating System (HOS). Low-frequency resonance emanating from wind-struck high-rise buildings triggers the erratic behavior in these units. To SV2 pilot Noa Izumi's relief, no copies of the software were installed in Division II's AV98 Ingram police Labors. They also learn that HOS programmer Eiichi Hoba, who had committed suicide days before, was obsessed with the Babylon Project's Biblical references (the Ark being alluded to Noah's Ark, for example; his own name. E. Hoba—Jehovah—for another) and planted a self replicating virus in the code that would cause Labors to malfunction. A computer simulation predicts that gale-force winds acting on the Ark could send all the Labors in Tokyo into a massive rampage, especially since the Ark's size and steel framework amplifies the resonance frequencies causing them to reach farther into the city. Worse, the weather bureau announces that a typhoon is expected to hit Tokyo within two days. Gotoh discreetly gets clearance from the TMPD leadership to destroy the Ark as Shige tries to dig up more evidence of Hoba's guilt to justify the operation. Kanuka Clancy returns from the US to help in the raid. Division II attaches flotation bags to their vehicles and head out to the Ark. Malfunctioning HOS-equipped Labors engage the team as soon as they land on the Ark. Ingram pilots Noa and Ohta, plus Kanuka in a hijacked AV-X0 TYPE-0[3] police Labor prototype, buys time for Hiromi, Asuma and Shinshi to break into the control room and activate the Ark's self-destruct sequence. However, Kanuka loses control over the TYPE-0 in the chaos because it runs on HOS as well. Trapped by the TYPE-0 in one of the last remaining ledges, Noa climbs out of her damaged Ingram and fires her shotgun into the Labor’s S-RAM[4] system to finally shut it down. With the successful destruction of the Ark, SV2 sends helicopters to rescue the team.
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