Yuji Nimura and Mamoru Arita are co-workers at a hand towel factory. Mamoru is always concerned about Yuji who cannot relate with others well and Mamoru suggests Yuji to have secret hand signals between them. “If I do this (by pointing his thumb to himself), it means ‘Wait,’ and this means (by pointing his forefinger to others), ‘Go ahead.’” In his apartment, Mamoru takes good care of deadly poisonous jellyfish which can kill humans. One day, while Yuji is visiting him, the head of the factory, Fujiwara, suddenly comes in. While Mamoru keeps listening to Fujiwara’s usual boring stories even with smile on his face, Yuji cannot hide his irritation toward Fujiwara. However, when Fujiwara finds the jellyfish in a water tank and put his hand inside, Mamoru holds Yuji from warning him and just stares at Fujiwara silently. Fujiwara pulls his hand out of the water tank by sensing danger by instinct.

The next day, Fujiwara fires Mamoru for not warning him. Mamoru leaves the factory with giving the signal “Wait” to Yuji. At that night, Yuji gets frustrated and a sudden violent impulse drives him to rush to Fujiwara’s house with an iron pipe in his hand. When he arrives at the house, he finds the couple’s bloody dead bodies. Going back home without knowing what happened, Yuji frantically tries to call Mamoru in the darkness, but there is no answer.

In the meeting room in prison, Yuji blurts out, “I should’ve killed them first.” Mamoru replies violently, “Shut up! When I say “Wait”, you wait, did you forget?” Mamoru is concerned more about his jellyfish which he gave to Yuji, than his own situation. Shinichiro Arita, Mamoru’s father, visits his son after the long estrangement resulted by his divorce from his wife. Shin-ichiro awkwardly tries to talk with his son and Mamoru thanks him for his visit. This is the reunion of the father and son after five-year separation.

In the meeting room, Mamoru seriously begs Yuji to acclimate his jellyfish to fresh water, so it could survive in Tokyo. Yuji desperately confesses that he will wait for Mamoru forever until he will be released from prison. However, in reply, Mamoru yells at Yuji, “Then, it’s all over. Don’t come here anymore.” Feeling helpless, Yuji violently crushes the water tank and the jellyfish slips down from a hole on the floor.

When Shin-ichiro visits Mamoru again, Mamoru coldly talks about his execution. After that, Mamoru kills himself in a cell by tying up his forefinger pointing as “Go ahead” signal. Around the same period of time, Yuji wakes up in his apartment and tears up floorboards as if he is tempted by something. He finds a luminous jellyfish swimming in darkness. Yuji is excited and the next day, he rushes to the prison to report this to Mamoru.

Yuji finds Shin-ichiro leaving the cemetery with ashes of Mamoru and follows the old man to help his recycling factory. Yuji acts like pursuing Mamoru’s will and he drops jellyfish foods, brine shrimp, into the river on the way of his delivery works. Yuji seriously tells Shin-ichiro, “I know Mamoru’s jellyfish is somewhere in Tokyo.” Shin-ichiro cannot believe that jellyfish which needs saltwater, can be lived in fresh water rivers in Tokyo.

One afternoon in pouring rain, Yuji discovers jellyfish again in an abandoned garage where Yuji and Shin-ichiro sheltered themselves from the rain. While Shin-ichiro is surprised at seeing jellyfish, Yuji remains calm as if he expected to find it.

Mamoru is standing next to Yuji while he is falling asleep at the recycling factory. Shin-ichiro cannot see Mamoru, either. Mamoru curiously glancing around the factory and suddenly cuts out the electricity for breeding the brine shrimp for unknown reason. Waking up, Yuji gets upset by the broken breeding machine and in anger tries to grab money from a safe by blaming Shi-ichiro. Shin-ichiro stops Yuji and asks him, “Why can’t you try facing this reality?” Yuji rushes out of the factory. Shin-ichiro follows Yuji, but he cannot find him anywhere.

Desperate Yuji invites young boys whom he met at the game arcade in midnight to sneak into his sister’s husband Takagi’s company and steal the money. The boys are quickly arrested by police who are called in by the alarm. Yuji alone manages to escape and returns to Shin-ichiro’s factory. Shin-ichiro accepts Yuji by saying “I forgive all of you”. On TV, the news reports that massive numbers of jellyfish appear in rivers in Tokyo. When Shin-ichiro finds a large school of jellyfish heading for the ocean, he thinks that Mamoru’s wish comes true and follows them endlessly.

Yuji left the factory with the memory of Mamoru. Mamoru is now standing next to Shin-ichiro working alone in the factory. In the town, the young boys hang around the restaurant and do nothing. After a while, they suddenly started walking powerfully toward somewhere.
 

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