The movie will focus on Ai Haibara's past and will reconstruct the Mystery Train arc from the television anime, which shows Haibara and Conan meeting for the first time. The movie will also include scenes from the Kurogane no Submarine (Black Iron Submarine) movie.

After the events of the 1st series, Fenarinarsa continues to drift from Earth, so the King asks for help from the kingdom, Marinarsa, to send their daughter, Momo (Who is identical to the 1st one) to Earth to regain humanity's faith in their dreams.

The anime follows a group of friends Giulia, Maria, Enrico, Lucio and Angelon during the disaster as they team up with a Japanese journalist Shiro Ando, and begin their own investigation of what's occurring (during the week long period of exposure when the ICMESA refused to notify citizens of the poison). As many animals are dying and people are getting sick. The children and Shiro discover deadly dioxin was released and inform Enrico's father, the town mayor, who evacuates all the citizens. Shiro continues investigating more and learns of the negligence of La Roche, a company who controls ICMESA. La Roche knew they were in violating of existing safety laws/protocols and destroyed evidence of their crimes. The children attend a press conference to ruin La Roche's reputation as the destroyed proof might not be enough in a court of law to punish them. Giulia's pregnant sister, who opted to not abort, gave birth to a healthy girl. The happiness is short lived, as the baby prematurely dies from dioxin poisoning.

Hatanaka Kosaku, a hopeful boxer, has a mean KO punch. Unfortunately, his dietary willpower is weak, and he eats even greasy hamburgers right before a bout. As a result, he has to compete in higher weight classes, and as soon as he takes an abdominal punch, he vomits, which causes him to lose the match in shame. As he tries to grapple with his weak will, he meets Sister Angela, a novitiate at a local convent. While Sister Angela strives to help Hatanaka in his endeavor, he seems to make her training to be a nun more difficult.