It's day one of the formation of the the second division of the Special Vehicles Unit 2 (SV2). Unfortunately the team seems to be a bunch of misfits. Noa, a girl that loves labors a little too much; Asuma, a cadet who doesn't want to be there; Oota, a gun maniac; Shinshi, a hen picked husband; and Hiromi, a gentle giant of a man. Leading this squad is Captain Gotoh, a man who seems rather laid back, but is quite a strategist and an excellent cop. Soon they are dispatched to apprehend an armed terrorist Labor, but first they'll need to retrieve their Patlabors en route to the crime scene from the middle of a traffic jam...

The mayor of New York is coming to Tokyo to inspect the Babylon Project - a long term land fill project to reclaim Tokyo Bay. All of the Tokyo Police force are assigned to protect the mayor including the SV2. To help them, the New York Police force has sent Kanuka Clancy, an American-Japanese woman who immediately causes suspicion amongst the SV2, and much interest amongst most of the male squad members. The SV2's mission is mainly for show, but they soon find themselves in the middle of a terrorist plot!

A series of incidents occur in Tokyo Bay including a damaged undersea cable, and a car being pulled off a pier. Could this be the work of an actual sea monster? Detective Matsui of the Metropolitan Tokyo Police Department asks Captain Gotoh for help. Shige and Sakaki help pilot a remote control Labor, to search for what caused the incidents.

The SV2 are called upon to help with a hostage situation at a video shop, but Oota's temper gets the better of him, and he blows away half of the shop as well as stopping the criminals. Gotoh decides that his team need retraining and sends them back to the academy. They arrive but strangely there are no cadets there. The next day, after a night filled with strange events, Noa and Asuma ditch their training to go to the local shop. There, Asuma meets the shop owner, an old man he knew when he was a cadet. The old man tells him that an accident occurred several months ago. A young woman at a mock battle was hit and killed with a paint bullet from a Labor gun. Is the academy really haunted by her spirit?

The Second Unit are on vacation. Most of the team have a place to go except Gotoh, who just seems to want to hang around the office with Shinobu, and Asuma who decides to go to his father's factory. Meanwhile in Tokyo, a police road block stops a truck. One of the policemen become suspicious when they see a Labor under the truck's tarp. He asks to see the Labor's permit, but the truck runs the road block. The police give chase, but the Labor in the back of the truck fires upon them destroying all the police cars following. It is a Self Defense Forces Labor. Later that night, Gotoh calls Shinobu outside her house. He tells her that a truck with a military Labor ran a road block and shot up several police cars. With the Japanese military in the middle of war games, it will take several days for them to account for all their Labors. Are the military trying to stage a coup?

It is the second day of the siege, but the rebels have not made any demands yet. Kanuka, disguised as a delivery person, asks the mechanics for help. Sakaki tells Kanuka that the police academy has a Patrol Labor prototype they could use. One of the mechanics says he overheard one of the rebels say that have a nuclear weapon. Meanwhile Shinobu has a video conference with the police chiefs. They tell her that the US military will be coming to end the coup before it becomes a civil war, and she should step down. She tells that she won't give into their bluff, and refuses to carry out their orders. Disgusted by their actions, Shinobu forcibly leaves the conference after an officer attempts to take her into custody. Asuma and Noa arrive in Tokyo and Asuma tells Gotoh that he saw Kai in a restaurant in Hokkaido. Upon hearing the news, Gotoh thinks he has Kai's plan figured out. A short range missile has been stolen from the US military, and two ships have been hijacked and equipped with missile launchers. This means one of the launchers is fake, but which one?

A truck at a gas station is stolen, but when the attendant tells a passing police man, the driver of the truck doesn't want the police chase after it. The police suspect something fishy is going on and arrest him. He is in fact a member the terrorist group "Beach House". He stole the truck which was carrying a Labor from the Tokyo Labor show. The SV2 attempt to capture the truck in front of a tunnel, but the truck escapes with the help of the terrorist in the Labor, who breaks trough the trailer after not being able to get into contact with his friend in the truck. Later, the man who stole the truck drives off the highway only to discover that he is helping a terrorist. The theft of the truck from the petrol station was just a opportunistic crime to get a ride home. He's just a seasonal worker that doesn't want to be involved in this. Unfortunately for them Shaft will do anything to stop the truck and it's contents.