After conquering the galaxy, mankind has reached its apex and is now on a steady decline. The resources of the universe are diminishing, and around 500 billion humans begin to return home to Earth. Thus begins a war between the various factions of humans for control of the planet. Eventually, an authoritarian government known as the Gaia Sanction prevents the re-population of Earth. Captain Herlock was one of the Elite Wing who was tasked by the Gaia Sanction to defend the Earth. His fleet of ships was unstoppable under his command. However, the Gaia Sanction allows a diplomatic elite to immigrate to Earth, which angers Herlock. He goes rogue and fires upon the diplomats and the rest of his fleet. He decides to unleash dark matter on the planet to make it uninhabitable, but also becomes engulfed in it which immortalizes him. One hundred years have passed, and the legendary Captain Herlock is still at large, with only the Arcadia under his control. The Gaia Sanction continues with their plans for control over the Earth, while hiding its true state. But Captain Herlock is preparing for one final showdown with them, which will determine the fate of the world!

The luscious hills of Koumi Island are one of many reasons tourists pay its shores a visit—a reason that comes second only to its scenic coral reefs and the legend of Anne Bonnie and Mary Read. The museum that houses the cutlass and pistol of the daring pirate duo does wonders for the small island's tourism. 

On a trip to the island, the famous Kogorou Mouri is joined by his daughter Ran, her best friend Sonoko Suzuki, the Detective Boys, and Conan Edogawa. Following a mix up at the hotel regarding their rooms, the group encounters treasure hunters and becomes acquainted with the island's treasure fever. Sent on a hunt of their very own, the Detective Boys scour the isle; while in far harsher waters, Conan discovers a murder. The police, following a clue from a recent robbery, arrive soon after, and Koumi is plunged into chaos. 

What follows is a mad dash by not only the treasure hunters but also the inhabitants of Koumi to secure Anne and Mary's long lost booty. All the while, however, Conan, Kogorou, and the police search for the one thing far greater than riches—justice.

[Written by MAL Rewrite]

A video blogger attempts to fake cryptid sightings to boost his views, but gets more than he bargained for when his crew is slaughtered by a real monster. Elsewhere, students find themselves preyed upon by a sandworm-like beast, initiating a desperate struggle for survival on their own school grounds. With more of these attacks from mysterious creatures occurring, researcher Sousuke Banba tasks himself with delving into the mystery. With nothing but the keyword "Kagewani" to lead him, he scours the sites of recent attacks in hopes of finding a lead to eradicating the creatures for good. However, Sousuke finds that these threats to humanity are even closer to home when the pharmaceutical company, Sarugaku, starts to encroach on his investigation. [Written by MAL Rewrite]

On a dark night, the Japanese police is raided by a spy. Different countries' intelligence agencies—such as England's MI6, Germany's BND, and America's CIA—as well as the FBI's secret files are going to be taken, but public safety officers lead by Tooru Amuro arrive just in time. The spy steals a car and escapes. The spy and Amuro are then locked in a dead heat on the highway, and just as it is about to cause an accident with multiple cars, the spy's car is hit by FBI agent Shuichi Akai's rifle bullet and falls of the roadway.
The next day, Conan and his friends go to a newly-remodeled aquarium in Tokyo. Under the main attraction, a Ferris wheel, Conan finds an attractive woman alone and injured. Her left and right eyes are different colors.

But the woman is in a state of amnesia where she doesn't even remember her own name, and the cellphone she's carrying is broken. Conan and his friends promise to help her regain her memory, so they stay with her.

Throughout all this, Vermouth is watching behind the scenes. Afterwards, she pulls out a silencer and speaks into an attached intercom, "It's as planned, Gin."