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. 

The four members of Milky Holmes are going on a study tour. While soaking in the hot springs among snow monkeys, alarms interrupt the relaxing environment! It was the work of the Thief Empire. A fierce battle between Milky Holmes and the Thief Empire begins, with both sides using their Toys (special powers). Furthermore, with the arrival of the Genius 4, a three-way fight occurs! In the midst of battle, a violent lightning strikes from the sky. Struck by the lightning, the four Milky Holmes girls lose their abilities.

Obata Yousuke lives on Pagopago in the Fiji archipelago with his father Tetsuo, a specialist in oceanographic biology. After a storm strikes the island, Yousuke rides to the lagoon with his Jet Ski and finds a strange baby dinosaur there. He takes it to his father's laboratory and names it Coo. Coo grows and seems to be a large marine reptile (a baby plesiosaur) which lived there some 65 million years ago. But Coo soon becomes an object of interest for the French secret service, assigned to protect the nuclear interests of France in that otherwise peaceful part of the world.

Silent Sky is a combination of the additional episodes 13 and 14. It consists of the story in the future, three months after the incident that was similar to "New Generation Madness" and the disease Chaos Child Syndrome that brought by the past earthquake in Shibuya.