Kodaka compared the theory of whether or not she is dead or alive to Western villains like the Joker who are continuously brought back to life.

At the time of Danganronpa: Trigger Happy Havoc, Junko has Mukuro pose as her so that she may die in her place in a moment of "Ultimate Despair", while she uses her Monokuma persona to embark on her killing game.

Junko additionally manages to cheat her own self-imposed execution by having her mind converted to an artificial intelligence at the moment of her original death.

[15] In the first game, Danganronpa: Trigger Happy Havoc, Junko fakes her death by having Mukuro pose as her so she can kill her under her Monokuma guise, using the event to encourage her former classmates at Hope's Peak Academy to participate in a "killing game", both actions serving to feed her desire to fuel an "ultimate despair" within herself and them.

[15] Throughout the game, Junko (in the form of a robotic teddy bear dubbed Monokuma) provides various motives to turn the students against one another, overseeing the subsequent class trials and performing the various executions while broadcasting the events to the world at large, culminating in her presenting Mukuro's corpse in an attempt to frame the "Ultimate Detective" Kyoko Kirigiri without breaking the rules she set for herself for the "killing game", and ultimately agreeing to execute herself after being exposed as the mastermind.

In Danganronpa 2: Goodbye Despair, Junko is revealed to have used Chihiro's Alter Ego technology to transfer her consciousness into Monokuma at the moment of her death as an A.I.

In the climax of Danganronpa Another Episode: Ultra Despair Girls, set between the first and second games, the Monokuma variants Shirokuma and Kurokuma are both revealed to be under the control of Alter Ego Junko, before they are both destroyed by Izuru Kamukura so he can bring it with him to Jabberwock Island, setting up the events of Danganronpa 2: Goodbye Despair.

[16] Junko appears in a cameo appearance in the third main series installment, Danganronpa V3: Killing Harmony, in the bonus minigame "Ultimate Talent Development Plan", with the game's main storyline, set in a world where-in a Dangaonronpa reality television show based on the fictional Danganronpa franchise has been hosted yearly for 53 years within an otherwise violence-free futuristic utopia, seeing the mantle of Junko be assumed by the series' showrunner each season.

In the "Despair Arc" of Danganronpa 3: The End of Hope's Peak High School, set before the events of the first game, Junko is collected from the airport along with Mukuro to a limousine after she blows up her taxi.

Later, Junko addresses Chiaki via a monitor and traps her inside a test course for her "punishment" center, intended to induce the rest of Nagito's class to her cause via brainwashing.

Several months later, shortly before the events of Danganronpa: Trigger Happy Havoc, Junko and Mukuro assist their class in converting the academy into a bunker to protect them from the chaos outside, while secretly preparing to have them detained to begin their killing game.

[40] Junko and Monokuma were collectively named as the "Most Popular Game Character for Cosplay" in the Guinness World Records Gamer's Edition in 2018.

[42] Thanasis Karavasilis from Manga Tokyo was also pleased with Junko's return but felt the other characters from the Despair Arc managed to be as entertaining as her.

[43] Kotaku claimed that Hajime's transformation into Izuru and his team up with Junko served as one of the biggest attractions from the anime's Despair Arc.

[45] Destructoid called Junko the best character in the entire franchise for how she embodies the themes often discussed in the series by the cast and how due to popular demand, her legacy continues in following installments despite her death.