It's made clear when she calls the first peaceful and happy year the class spent together at Hope's Peak "the worst school life ever!" When she's voted to be executed, she's ecstatic because she gets to experience one of the ultimate forms of despair: having your evil plan to plunge humanity's survivors completely into despair backfire right as you were about to succeed, and then dying an incredibly cruel death to top it off. Bad is Good and Good is Bad: She loves despair and hates hope.
It takes the entire series before things start to clear up for the good guys with a "Ray of Hope" Ending. Even though Junko dies at the end of the first game via self-inflicted punishment, she dies having gotten everything she wanted. If she succeeds in her plans, the entire world is plunged into despair if she fails, she gets to experience the despair of having her plans come crashing down around her. In fact, by Junko's own description of her philosophy, she technically can't lose. The Bad Guy Wins: She wanted to feel the ultimate despair, and she got it.
It's also suggested that while Junko genuinely did love her sister, Junko killed Mukuro because it would mean feeling the rush of despair from a loved one's death. all while insulting Mukuro's accomplishments.
She also took pride on being the "better" twin during the final class trial in Trigger Happy Havoc by claiming to have surpassed her sister in every way. Junko belittles her sister Mukuro whenever she can, and kills her (or tries to kills her in IF) even though Mukuro was doing exactly what Junko told her to do.
Her Goal in Life is to drive all of humanity past the Despair Event Horizon to prove her point. While Junko is outwardly a Large Ham, she's inwardly a Misanthrope Supreme who believes that humanity is naturally inclined towards despair. From that point on, the Future Foundation is left to clean up the colossal mess made by her and Ultimate Despair. Being voted guilty during the final class trial in Trigger Happy Havoc, Junko gleefully committed suicide by executing herself. After the End, she ruled the world's remains, with Monokuma serving as her public persona. Aside from forcing most of Class 77 into becoming a Brainwashed and Crazy terrorist group called Ultimate Despair, Junko also masterminded the events which led to the Tragedy, leading to billions of deaths.