The movie is set three years after the events of the first movie. Noa Izumi and Asuma Shinohara are now working for Shinohara Heavy Industries. Isao Ota is a police academy Labor instructor. Mikiyasu Shinshi had been reassigned as the Tokyo Metropolitan Police's head of General Affairs. Seitaro Sakaki retired with Shigeo Shiba taking over his position as head of the labor maintenance team with Hiromo Yamazaki, Kiichi Goto and Shinobu Nagumo remaining with the unit as Kanuka Clancy had permanently returned back to New York. Most of them had been replaced by fresh labor pilots.
Suspicious events begin to materialize with the face of a military takeover of Tokyo by JGSDF forces and declared Martial law after the Yokohama Bay Bridge was destroyed by a missile, with belief that the JASDF was the culprit. Protests in various JSDF bases took place as a means of conveying their denial of the Yokohama Bay Bridge attack. Before long, public panic came with the attack on several bridges in Tokyo Bay and various communication centers with SV2 headquarters, supposedly by JGSDF-marked gunships with the release of a supposed deadly gas after Special Assault Team snipers shot an auto-piloted blimp that was responsible for jamming all electronics in the Greater Tokyo Area.
Goto and Nagumo once more assembles the original Section 2 members in a hidden subway passage as they embarked on a secret operation to apprehend Yukihito Tsuge, the mastermind of the terrorist attacks in the Greater Tokyo Area and a JGSDF officer who had gone AWOL after the disastrous UN Peacekeeping operation in Cambodia back in 1999. When the JSDF and the police couldn't see that Tsuge was the culprit for bringing confusion into Tokyo, Goto and Nagumo authorized an operation to capture Tsuge after seeking assistance of a JGSDF intelligence agent named Shigeki Arakawa and the ex-officers of SV2 without backing from the Tokyo Metropolitan Police Department. Tsuge was eventually arrested by Nagumo herself after she and the other original Section 2 members were able to storm an artificial island used as his hideout.