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Participation in the Second Nonary Game
Junpei's bracelet number is 5; he has no alias due to his childhood friend June blurting out his name before code names were decided. Her nickname for him is "Jumpy". He quickly becomes the defacto leader of the group and (as the player) is typically the problem solver for all situations he is present for. He has a profound desire to protect June from harm, and can occasionally be clueless about her affection for him.
Other than his connection with June, Junpei has no prior association or awareness of the Nonary Game or Cradle Pharma. He was abducted from his home by Zero, and awakens in a ship cabin which immediately begins flooding. As the protagonist, his ignorance serves to represent the player as context and clues are steadily revealed.
Junpei shares a psychic connection through morphic fields with June, an ability he is not aware of. He has flashes of inspiration and knowledge which he should not be aware of from playthrough to playthrough. The game uses its New Game+ trope to justify this awareness within the context of the storyline.
Participation in the Third Nonary Game
After escaping from the Nevada facility where the second Nonary Game had taken place, Junpei spent the following years searching for June, who had vanished after the events of Nine Hours, Nine Persons, Nine Doors. Some time after the release and spreading of Radical-6 (a mysterious airborne disease) and the subsequent destruction of several "annhihilation reactors" that severely damaged the whole planet, Junpei finds a newborn orphan who he names Quark. Junpei adopts Quark as his step-grandson and becomes a scrapper to get by.
He is eventually approached by Zero Sr., who offers him the chance to reunite with June in exchange for his participation in the third Nonary Game, to which he accepts. He enters the game under the alias of Tenmyouji, bringing Quark with him and playing a pivotal role in the events of Virtue's Last Reward.