Takoshima's main industries are rice farming, fishing, and high tech industry. The Takoshimese Military is known to have an Army with advanced laser weaponry (in the form of special laser tanks). This nation seems to be the most disorganized of all the mentioned ones (America, England, Russia, Takoshima) and is mostly divided up based on what faction owns what location (police, military, KGB, Black Ninjas, White Ninjas, East Yakuza, West Yakuza, etc.)
Crypto and Natalya Ivanova arrive in Takoshima to find out information on Project Solaris. Natalya gets word of a protected package being delivered to a KGB official in Takoshima City, but due to Natalya's defection of the KGB, she herself is unable to get it. Crypto goes into Takoshima City, disguises as a KGB agent, and obtains the package from an official. However, an agent informs of the package's disappearance, causing a giant manhunt to go on in the city.
Crypto meets Natalya at the back of the Zen Temple. She opens the package, which contains information about Project Solaris. According to the paper, the project is being headed in a hidden base on the island. However, as she reads the paper, the KGB discover the two and attack. Crypto and Natalya battle their way out of the base, with Natalya making her escape from her car.
Back in Takoshima City, Orthopox tells Crypto that the White Ninjas clan, who worship the Furons, are about to give information about a Furotech Cell. After listening to three radio broadcasts, Crypto meets the White Ninjas at the back of the Zen Temple. The leader recognizes him as a Furon, and proceeds to challenge him to a quiz. Once Crypto successfully finishes the quiz, a group of Black Ninjas intrude the base, leading to a battle. Crypto manages to overcome the Ninjas, with the White Ninjas, now believing Crypto to be a true Furon, handing him over the Furotech Cell for the Ion Detonator.
At Sashimi Village, Natalya then reveals that a scientist called Dr. Go!, a former KGB scientist who has been captured by the Black Ninjas for defecting, may help Crypto reveal where the KGB's base is. He finds Dr. Go! at Castle Kuro, where he manages to help him escape the building from the KGB and Black Ninjas. The White Ninjas come to rescue Go!, allowing Crypto to destroy the castle. He then meets Go! in Takoshima City. He reveals that the base is inside Mt. Seiyuki, but that access requires a password. Go! reveals that he wrote the password on a torn picture he gave to his former girlfriend Professor Yuki and her boyfriend Sascha Soysorski, but his piece was taken by the Black Ninjas. Once he obtains the two pieces from Yuki and the Black Ninjas, he then destroys the KGB Building, luring Sascha out. Sascha is then killed by Crypto, who takes the piece of the picture, revealing the passwords to be "Eye", "Love" and "Ewe".
Now having the passwords, Crypto hands them to Natalya, and they proceed to storm through Mt. Seiyuki, fending off the KGB agents. At the top of the volcano, they access the secret base. On a large screen, USSR Premier and KGB leader Milenkov appears, telling them that the KGB are about to destroy Takoshima using Kojira, a former summer secretary who has been transformed into a giant Kaiju mutant. The two manage to escape the base before it's self destruction.
Crypto then meets Pox, who tells Crypto about a trail coming from the ocean of Takoshima. As Crypto follows it from his Saucer, the trail reaches land, revealing that it is Kojira. Kojira then proceeds to attack from the city, leading to a large battle between military forces and Crypto. Eventually, Crypto overcomes Kojira, causing the Kaiju to faint and revert back to her human form. Natalya meets Crypto nearby, informing him that the KGB's attention has shifted to Tunguska, her homeland. After this, Crypto leaves Takoshima for Tunguska.
Takoshima City: The capital and urban center of Takoshima. The city occupied most of the north-west and most of the civilian population lives there. The KGB, West Yakuza, and East Yakuza all have bases on the outskirts. The main landmark is a spoof of the Tokyo Tower. The city was destroyed by (depending on how the player played the last mission in Takoshima) Kojira/Cryptosporidium. However, enough civilians and resources survived to allow the city to be rebuilt.
Red Tower: A spoof of the Tokyo Tower in the center of Takoshima City. Two Yakuza stand guard there, suggesting that they own it. However, in one mission, the KGB is seen there.
Red Tower Underpass: An underpass in front of Red Tower.
KGB Headquarters: A large building in eastern Takoshima City. The building was destroyed by Cryptosporidium in an effort to kill Agent Soyorski.
KGB House: A house south of South Street (the street south of Takoshima). The house is owned by the KGB, as several Agents operate from there.
West Yakuza Compound: A building in west Takoshima City, with light walls made of dumpsters surrounding a plaza. The West Yakuza are concentrated inside.
East Yakuza Compound: A building in east Takoshima City, with reinforced walls (the dumpsters themselves can't be moved: a car has to be pushed into them, or they have to be destroyed). More or less the East Yakuza equivalent of the West Yakuza Compound.
Shinobi Island: An island north of Takoshima City, where the Black Ninja's main base is.
Shinobi Bridge: A bridge from Takoshima City to Shinobi Island. The bridge is, on the Shinobi side, guarded by two Black Ninja.
Gouka Road: A small road crossing south Takoshima. Ninjas constantly attack citizens here: the attacks never stop, meaning that no matter how many Black Ninjas die or how long somebody waits the fighting won't stop. Similar to Tarkovskoye in Tunguska (see Tunguska).
Continental Road: A large road spanning middle Takoshima, connecting Takoshima City to the Zen Temple.
Upper Clearing: A span of land that is not paved, but is clear enough that you can cross northern Takoshima from Takoshima City to the Zen Temple. It doesn't move much.
Arkvoodle Camp: A large camp with around 15 tents south of the Gouka Road and north of Castle Kuro. A rather diverse population of Cultist lives here, including even policemen.
Sashimi VIllage: A village east of the Gouka Road and north of Mount Seiyuki. The village is populated by Rurals (Urban men who carry baskets on their backs).
Castle Kuro: A castle on a mountain, on the western peninsula. KGB and Black Ninja both own the castle. Cryptosporidium destroyed it after rescuing Dr. Go!
Military Barracks: A barracks along the Gouka Road, in central Takoshima. Over a dozen well-armed soldiers guard it, along with three ground turrets.
Small Compound: A compound southeast of the Military Barracks. The Ninja have a very small presence there.
Mount Seiyuki: A volcano on the eastern peninsula. A path snakes around it, with three terminals only accessible by code words (eye, love, ewe). The entrance is at the top (the volcano's mouth) and leads to a central room connected to a mass of bridges held up by cables. The exit is a large opening in the side of the volcano at the end of these bridges, where one trying to leave can used a jetpack to fly onto the volcano. The base was destroyed after an assault on it.
Zen Temple: A temple in northeastern Takoshima. Both civilians and White Ninja go there, and it is a gathering spot for the Cult of Arkvoodle. The ceremony that brought about the Second Coming of Arkvoodle took place there.
White Ninja Compound: The White Ninja base, located east of the Zen Temple. An Arkvoodle Cult gathers there.
- The city's name most likely comes from the city of Tokushima, Japan.