The story opens with a high school by the name of Ageha Yoshina, as he is heading home from school one day. Ageha goes comes across a public pay phone that is ringing by itself. Curious about this, he picks up the phone and realizes there is no one else on the other line, but when he hangs up he finds a red calling card with the word "Psyren" printed on it. The next day, Ageha notices one girl at his school by the name of Sakurako Amamiya who has become a very cold and mysterious girl. When they were younger Ageha experienced the death of his mother and Sakurako had been the nice and caring one who tried to be there for him to get through such a difficult time. Nobody at school talks to her and he sees that several of the other girls took her wallet and hid it outside on her. Ageha decided to take it back to it's rightful owner which Sakurako is grateful for, but before giving it back to her, he notices inside her wallet is the same exact calling card he had found the day before. He questions her about it, but she quickly denies what he says and acts like she has no idea what he is talking about. Sakurako then immediately runs out and disappears.
After the incident with Sakurako, Ageha begins hearing about the many disappearances all around the nation and that there is a "Secret Society of Psyren" which is led by Nemesis Q. This place is supposedly one for those who are sick of their current society and wish to go to a place of "Paradise." Anybody who can find out the truth of Psyren will be rewarded with 500 million yen, which interests Ageha highly. He learns he could make possibly 5 million yen by bringing his red calling card out to the public, but decides against that because he thinks of how Sakurako disappeared, and wants to find her and save her from the place she has been taken to. Ageha then uses his card at the pay phone he had recieved it at and when he places it inside the phone rings, and he answers. The voice on the phone tells him to answer questions for an examination which he does, but toward the end the questions become more personal about his life. He becomes irritated and the voice screams at him which he then retaliates, but giving the phone his name. Afterward, Ageha is asked one final question: "Would you like to go to Psyren?". He instantly thinks he's being fooled and answers no, before leaving to head back home. With the phone hung up, the voice says the examination is complete and they will contact Ageha with the results.
The next day two men are examining the pay phone that Ageha had used last night and find out who had used it, and they make there way to the school, to find, and speak with Ageha Yoshina. The men inform the school that they are investigators with the police and would like to speak with Ageha. However, Ageha learns from his sibling Hiroki that the two men are not police, and so he quickly leaves the school before they find him. Just as he jumps over a wall the two men appear and inform him that they have been phone tapping calls to learn anything about Psyren that they can. They demand Ageha to hand over his red calling card, but Ageha makes it clear he's not handing it over without a fight, and the three brawl. They eventually pin him down where one of the men tell him that Psyren is in fact a real world and that he needs the card to reach the place. Ageha has no intention of handing it over and manages to break free and escape from the two, but they catch up and corner him in an alley way. The men need the card before it awakens on them, and as they go to take it from a blinded Ageha, who had been sprayed in the eyes by some type of chemical, he begins to hear a ringing and checks his cell phone which is from a Restricted Caller. Before the two men get to him, Ageha answers the call and as he does Nemesis Q flies down from above and Ageha is instantaneously transported to the other world. The world of Psyren.