The movie is set on a state-of-the art Aegis vessel with the full cooperation of Japan's real-life Ministry of Defense and Maritime Self-Defense Force. The corpse of a Self-Defense Force member has been found — minus the left arm — and a spy has infiltrated the Aegis vessel. The heroine Ran is put in jeopardy, and Conan is forced to stand up against the dangerous Spy "X."

On a dark night, the Japanese police is raided by a spy. Different countries' intelligence agencies - such as England's MI6, Germany's BDN, 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.

After a sudden explosion at Edge of Ocean island in Tokyo, Tōru Amuro, codename Zero, begins to investigate. Meanwhile, private eye Kogorō is arrested as a suspect, so Conan Edogawa conducts his own investigation to prove his innocence, but Amuro stands in his way.

Ran’s secret past revealed! Ten years ago, something happened between her mom and dad. Now, plagued by nightmares, Ran is starting to remember… Meanwhile, a murderous card dealer breaks out of jail to seek revenge. His target: Ran’s father. Can Conan stop him in time and save his girlfriend’s family?

Ash meets the Mythical Pokémon Volcanion when it crashes down from the sky, creating a cloud of dust—and a mysterious force binds the two of them together! Volcanion despises humans and tries to get away, but it’s forced to drag Ash along as it continues its rescue mission. They arrive in a city of cogs and gears, where a corrupt official has stolen the ultimate invention: the Artificial Pokémon Magearna, created 500 years ago. He plans to use its mysterious power to take control of this mechanical kingdom! Can Ash and Volcanion work together to rescue Magearna? One of the greatest battles in Pokémon history is about to unfold!

In the underground Diamond Domain, where many Carbink live, the Mythical Pokémon Diancie serves as ruler. The Heart Diamond that sustains the land is beginning to fall apart, and Diancie is not yet strong enough to create a new one. While seeking help from the Legendary Pokémon Xerneas, Diancie encounters a group of thieves who want to take control of its diamond-producing power–and who awaken the Legendary Pokémon Yveltal from its cocoon in the process! Can Ash and his friends help Diancie discover its true power, stop Yveltal’s rampage, and save the Diamond Domain?

The Kingdom of the People of the Earth once ruled over the land, but now all that remains is the Sword of the Earth. in the city of Eindoak. Satoshi, Iris, and Dent arrive in Eindoak during a harvest festival's Pokémon Tournament and meet the legendary Pokémon Victini who wishes to share its powers of victory to someone. Elsewhere in the city, a descendant of the People of the Earth named Dred Grangil has arrived who seeks to revive the kingdom's power with the Sword of the Earth, bringing them back into power over the land, and Satoshi and his friends must stop him before he destroys the land along with Victini.

Ash and friends (this time accompanied by newcomer Dawn) arrive at an idyllic village on their way to their next Pokemon contest, where chaos will soon erupt with the prophecy of two Pokemon Gods (Dialga and Palkia) and the arrival of a mysterious, seemingly deadly Pokemon named Darkrai, which has the power to distort space and time.

Ash and his friends must stop a greedy media mogul from using the shape-shifting Zoroark to capture the time-travelling Celebi.

When the sadness of her father's disappearance gets to Molly Hale, she unknowingly uses the Unown to create her own dream world along with Entei, who she believes to be her father. When Entei kidnaps Ash's mother, Ash — alongside Misty and Brock — invade the mansion looking for his mom and trying to stop the mysteries of Molly's Dream World and Entei!

When Lawrence III's scheme to capture the Legendary Pokémon Lugia upsets the balance of nature, it is up to Ash Ketchum and his friends to save the world.

In the legendary past, before Poké Balls were invented, an aura-guiding hero Pokémon named Lucario sensed two groups of armies about to clash, and a threat of a massive war in front of Oldoran Castle in Kanto that would leave no survivors. He transferred this message to his master, the legendary hero Arlon, while he was being attacked by a violent group of Hellgar. During the battle, his sense of sight was lost and he was rendered unable to see. He used the detection of his Aura, and so with the offensive Wave Bomb, he eliminated them. Though by the threat, the queen of Rota, Lady Rin was resolute to die with her civilians, and so Arlon made a choice.

The Team Rocket leader, Giovanni, has found Mewtwo in a remote area of the Johto region. As Giovanni tries to re-capture Mewtwo, Ash and his friends are kidnapped by Domino, a new Team Rocket member, while trying to rescue Pikachu from Jessie and James. The Clone Pokemon are also captured and are then used as bait for Mewtwo. The situation then becomes a battle between the wills of Mewtwo and Giovanni; and Mewtwo also tries to discover if it and the clones have a purpose in life, even though they are products of science.

When the creator of the world, Arceus, comes to pass judgement on humanity for the theft of the legendary Jewel of Life, Ash and his friends are sent back in time to possibly reverse the events that led to Arceus' vendetta.

Two years after the events of the Fourth Great Ninja War, the moon that Hagoromo Otsutsuki created long ago to seal away the Gedo Statue begins to descend towards the world, threatening to become a meteor that would destroy everything on impact. Amidst this crisis, a direct descendant of Kaguya Otsutsuki named Toneri Otsutsuki attempts to kidnap Hinata Hyuga but ends up abducting her younger sister Hanabi. Naruto and his allies now mount a rescue mission before finding themselves embroiled in a final battle to decide the fate of everything.

High school student Hitomi is transported from Earth to the magical world of Gaea, where she meets boy prince Van Fanel, and is caught up in his quest to unite the countries of Gaea against the ominous Zaibach empire. On the way, she discovers an hidden ability and strives to unravel layers of mystery surrounding Van, his past, and the giant machine known as Escaflowne.

Precocious tween Karin finds herself abandoned by her father in rural Japan. Living in a temple with her grandfather, she meets Anzu, a giant "ghost cat" and notorious layabout tasked with looking after her. Distrustful of her new guardian, Karin sabotages Anzu's odd jobs for the townsfolk and befriends the eccentric local forest spirits. In an effort to win Karin over, Anzu accidentally makes a deal with the devil, and all Hell breaks loose.

As police inspector Yamato Kansuke pursues a certain man in the snowy mountains of Nagano, a shadow suddenly appears in his field of vision. While he's distracted, a rifle bullet fired by someone grazes his left eye and causes an avalanche accompanied by a roar. Ten months later, Kansuke, having miraculously survived the avalanche, receives a report that a researcher at the Nobeyama National Astronomical Observatory has been attacked.

コラボエピソード「乱歩邸殺人事件」は、劇場版「名探偵コナン 100万ドルの五稜星（みちしるべ）」にも参加した大倉崇裕が脚本を執筆。旧江戸川乱歩邸が物語の舞台となり、江戸川乱歩をめぐる難事件が発生する。 小林先生の引率で乱歩邸を訪れた少年探偵団。江戸川乱歩が書庫として使用していた土蔵には貴重な本が大量にあり、コナンたちは大興奮だったが、そこへやってきた佐藤刑事と高木刑事に近くの公園で殺害事件が発生したことを告げられる。事件の被害者の遺留品は普段公開していない土蔵に関係しているという。

When Giratina is discovered to be able to create parallel dimensions, it's up to Ash and his friends to stop a mysterious stranger from using its powers for evil.