Kenji Shiraishi is involved in the trafficking of illegal immigrants from China to Japan. One such case leaves an immigrant child to be an orphan. Instead of selling him along with others that arrived, Kenji flees with the boy to look after him and make an attempt at everyday life. The people after the boy, unexpected encounters with long-lost family members, and his vengeful nature are standing in the way of his future.

Yasuo is a gangster just released from jail. Believing his boss double-crossed him, enraged Yasuo is on his way to find the boss. But before setting out for the dangerous trip, Yasuo asks Kenji to take care of his mentally challenged sister, Yuri, and a mysterious black bag.

Eureka tells the story of an orphan who survives a traumatic experience when a bus he is on gets hijacked in rural Japan. The incident leaves him with survivor's guilt and post-traumatic stress disorder (PTSD). The movie explores themes of trauma, starting over, and the loss of loved ones. As the orphan tries to cope with his past, he forms a close bond with his cousin, who also experienced the hijacking. Together, they navigate through their shared traumatic experience and find ways to move on.