A platoon of military Labors and soldiers land in a forest. They are tracking down an experimental Labor. After a vicious battle, they manage to bring it down. They open up the hatch to find no pilot inside the cockpit.
One week passes. Division 2 is on constant alert after Division 1 are ordered to continue their training on the new AV-0 Patlabors. The work load is increasing, and on their last mission, a runaway berserk Labor restarts by itself after being stoped by a stun-stick. Asuma suspects something is wrong and investigates. He finds that the incidents started occurring when the new Hyper Operating System (HOS) for Labors was released by Shinohara Heavy Industries. Both the captains know about this. A military Labor that had HOS installed went out of control the week before, which is why tests are still being done on the AV-0's. Gotoh tells him a white lie that the Ingrams have HOS installed too (in reality Shige never installed the new operating system), so they might go beresk. This pushes Asuma to find out what the trigger is. While visiting the Shinohara factory with Saksaki, Asuma finds the HOS masterdisk. He discovers it has a virus in it. This means every Labor that has the new HOS, has the virus. The man who created HOS, Eiichi Hoba, committed suicide several months ago. It is believed that he purposely wrote the virus in the program to cause havoc.
Asuma eventually figures out that high-pitched sound is the trigger for the virus. With the help of Shige, they discover that buildings and other structures resonating together under the influence of a typhoon would cause thousands of Labors to self-start and go berserk, causing untold damage. Unfortunately a typhoon is due in Tokyo in the next couple of days. The main trigger would be the high-pitched noise coming from one structure; the Ark. The Ark is a tall, large platform like structure in Tokyo Bay that can service every Labor in Japan if necessary. If the structure is destroyed before the typhoon, the Labors won't cause havoc, as the sound pitch will not be high enough to trigger the virus. It is decided that Division 2, with the help of Kanuka Clancy, will go in secret to pull down and destroy the Ark. Unfortunately it won't be easy, and if they fail the blame will fall on their shoulders.