At night, a man and woman are parked near Tokyo Bay. The man goes out to get a soda, and when he returns, the car is gone. The next day, Ota prepares for target practice with a riot gun. Kanuka gives him the order to shoot, and he blows the target out of the water. Goto comments that the shotgun is dangerous and they shouldn’t use it, but Shige objects because he spent so much time assembling it. Sakaki and Shige then get a visit from Inspector Takahiro Matsui from Criminal Investigations. Matsui explains that with the recent cutting of an undersea Babylon Project cable and the sinking of an unmanned buoy, the department has borrowed a Nautilas underwater labor, but they don’t have any personnel who can operate it. Shige asks Matsui how he got involved, and Matsui explains he’s investigating a case where a woman and her car disappeared near Tokyo Bay. The woman was found alive and in shock on a beach, and Matsui adds that there were sideways tire tracks on the pier, as if something pulled the car into the water. Matsui asks them for help, and Sakaki agrees. At Tokyo Bay, Asuma asks a fisherman if he can really catch fish there, and the fisherman tells him he recently caught several creepy giant flounder. Asuma and Noa then wonder what’s going on when a man with an eye patch is forcibly thrown out of the Maritime Safety Agency building. Shige then tells them he and Sakaki won’t be going back because they’re helping with the Nautilas. Out in the water, the Nautilas is lowered underwater and Shige controls it remotely. With poor visibility, Shige slowly moves the Nautilas near the bay floor to search the area. Matsui spots something strange in the distance, and when the Nautilas moves closer, he sees that it’s the woman’s car. Something closes in on the Nautilas, but Shige can’t see anything. Suddenly, the connection to the Nautilas is lost. After the damaged Nautilas is retrieved, newspapers publish stories about a sea monster in Tokyo Bay. Asuma teases Noa that the bay is calling Alphonse, and Ota says he wants to get permission to use the riot gun. Kanuka thinks it’s nonsense because a sea monster wouldn’t come to a boring place like Tokyo Bay. She thinks it’s a whale, but Shige later tells Noa and Asuma there’s no way a whale could’ve taken out the Nautilas. He says the monster concealed itself and kicked up a cloud of mud. A package arrives, and Sakaki asks Shige what he’s going to do with dry ice. Matsui meets with Shinobu and Goto, and Goto suggests calling in the Self Defense Force. Matsui thinks that would set a bad precedent for the SDF coming in to keep the peace, so he asks SV2 for help. Shinobu says a sea monster is just the kind of case for Division 2 and thinks Goto should handle it.
In a TV news report, the government acknowledges that some unknown creature is in the bay. While eating lunch at a restaurant, Noa wonders if it really is a sea monster, but Kanuka insists that it’s a whale. Asuma comments that with all the strange elements so far, the only thing it needs now is a mad scientist. The man with the eye patch, Hirata, then comes in and places an order. Later, Asuma, Noa and Kanuka go with Hirata to the Hirata Biotechnology Laboratory, where he mentions the Panspermia Theory. Asuma doesn’t know what it is, and Kanuka explains that it’s a theory stating that life on Earth originated from space spores. Hirata says he proved it when 10 years ago he discovered organic substance alive inside a meteorite that was 450 million years old. Hirata thinks it’s a strange find because it dates from the Cambrian Period when many new species appeared on Earth. Noa questions if the organic substance was really part of the meteorite, and Hirata insists that he washed his hands before the experiment. Hirata explains that he performed genetic engineering experiments to trace the evolution of life on Earth. After several years, he finally created a life form that began to evolve. Hirata says that after eight years the creature turned to the reptile side and learned how to evolve, turning it into a monster. He thinks the pollutants in Tokyo Bay have caused further mutations, and he thinks the monster will lay eggs and endlessly reproduce, leading to an infestation of monsters that will eat humans as food. Hirata laments what he’s released onto the world, and when Noa asks how it got into Tokyo Bay, Asuma guesses that Hirata got scared and threw it away. Back at SV2 station house, the riot gun is loaded with shells, and Kanuka tells Ota he can go all-out since the monster isn’t a whale. Division 2 then mobilizes and heads to Tokyo Bay, and a mechanic tells Sakaki that Shige left earlier with his dried ice. A large crowd lines the road as Division 2 drives to the bay. As night falls, Hirata meets with Goto and says the monster will try to swim up Sumida River to spawn. Shinshi picks up the creature on radar, and Ota readies Unit 2‘s riot gun. Goto says he didn’t give permission for Ota to use it, but Kanuka says it’s ok. Asuma tells Noa to cut loose on the monster because he wants to see it go berserk. The monster then disappears from radar, and Hirata says it must’ve dived into a hole. Hiromi suggests running a high voltage charge into the river’s mouth, and Hirata says it could capture the monster, but it would also kill many fish and damage undersea cables. Asuma suggests using the Ingrams’ external speakers to create ultra high frequency sounds, but Hirata points out that certain wavelengths can accelerate egg laying. Noa then suggests that Hirata reason with the monster, but he says if it’s smart, it may curse him for bringing it to life. Shige then appears on a small boat with an oxygen destroyer, and Sakaki yells at him for making a stupid pipe with dry ice. As they struggle, the pipe falls into the water and lures the monster out. Police run away from the bay, and the human-shaped monster appears at the shore, featuring an uncanny resemblance to Hiromi. Hiromi runs over to get a closer look at the monster, and it looks at him. After a while, the monster leaves and heads for the open sea.
This time, SV2 is called in to investigate a mysterious monster causing several incidents in Tokyo Bay. If that story sounds familiar, it’s because the story from this episode and the manga also served as the basis for the 2002 movie WXIII: Patlabor the Movie 3. However, in this episode it’s played in a much more comedic fashion, with a mad scientist who eerily resembles Goto and a sea monster that looks like Hiromi. This episode also introduces us to Inspector Matsui, a mainstay of the Patlabor universe who pops up now and then to assist Goto on certain investigations. The silly portrayal of a sea monster here is quite a contrast from the serious portrayal seen years later in WXIII, so it makes for an interesting comparison between the two, especially since Oshii didn’t direct the third movie.