Accused of terrorism and feeling the heat, Saki's high-tech crew is in the crosshairs. Meanwhile, the shroud of mystery covering Takizawa is lifted as he and his fellow Selecao make their final moves. Every game must come to an end. For those playing Mr. Outside's twisted game of conspiracy thrills, the end comes now.
The story takes place in the year 2034, two years after the events in Ghost in the Shell: S.A.C. 2nd GIG. Female cyborg Major Motoko Kusanagi has left Public Security Section 9, an elite counter-terrorist and anti-crime unit specializing in cyber-warfare, which has expanded to a team of 20 field operatives with Togusa acting as the field lead.
A new member from the Black Organization that shrunk Shinichi's body manages to find out about Shinichi's transformation into Conan. This discovery starts to put those around him in danger as Gin and the other Black Organization members start to take action.
A large scale catastrophe is occurring across the planet. Ability users are discovered after the appearance of a mysterious fog, apparently having committed suicide, so the Armed Detective Agency sets out to investigate these mysterious deaths. The case seems to involve an unknown ability user referred to as "Collector," a man who could be the mastermind behind the incident.
Trust and courage are put to the test in order to save the city of Yokohama and ability users across the world from the grip of Collector where the Armed Detective Agency forms an unlikely partnership with the dangerous Port Mafia.
It’s a high-stakes mystery on the high seas! Enjoying a free prize cruise on a military ship, Conan and his friends find their relaxation interrupted by the threat of possible explosives on board! It’s a race against time to find the culprit and save the ship — and potentially the whole country!
A mysterious suicide and a series of unmanned robot run-aways sparks off a Police investigation into the suspicious software on-board thousands of industrial robots around Tokyo.