In the worst ending, everyone dies in their executions.
In the slightly better ending, after the executions are over, the students are left on their own. Hiiro and Esora leave, someone has to look after Marika and Saori, and the others are furious and helpless. They want revenge, but the game is over. Esora is even more bent on revenge in light of Rei's death, and Hiiro knows that she's done all she can do. This is the best outcome. Now all she can do is move on.
In the good ending, Nozomi comes to the rescue. Just as Hiiro finishes explaining that Rika attacked Saori and Marika to get them out of their executions, and that she guaranteed she would not survive her own execution because of it, Junko returns, having been temporarily cast out of Hope's Pinnacle when Rika first unleashed her firepower.
When Rika struck Saori and Marika, it also struck the monitor Junko was using to broadcast in on. Junko wasn't happy about Hiiro and Rika's deceit, but before she could do anything, Nozomi also hacked in. As an Ult. Hope, Nozomi felt compelled to crush Junko, an Ult. Despair. Before she can kill the rest of the students, Towa talks to her, imploring Noa Fukushima to remember who she was.
In the best ending, Nozomi reveals that she didn't come alone. Lumina Ichihoshi, Chiaki Nanami, and Alter Ego helped her hack in. There were also other humans trying to break into the academy alongside Nozomi and the AIs and those humans were: Unichord, Abyssmare, Masaru Damon, and Shinobu, all riding in on a giant mecha from Masaru.
After Shinobu escaped her execution, she eventually landed in Towa City where Unichord helped her find the likes of Komaru, the survivors of Makoto's game, the Warriors of Hope, and representatives of the Future Foundation (Abyssmare). They also receive help from Hajime and his survivors thanks to Shinobu's history with, and similarities to, Chiaki.
Because Lumina was designed to be an Ult. Hope and an Ult. AI, she and Nozomi are able to completely delete the Junko bothering them at Hope's Pinnacle. The students also declare new Ult. Hopes at this time, all of which were listed in a different post. Esora declares that Rei is her personal Ult. Hope.
Epilog: In time, Hope's Pinnacle is restored and Esoran and Nyochio become the new headmasters. Call of Artemis and LMO transfer from Hope's Peak to become the core 8 staff of the new Hope's Pinnacle with the core 6 units acting as the pilot class. (This occurs after Hajime and crew flee to Jabberwock while Makoto takes over Hope's Peak).
Every D4 student is able to attend because, with their consciousnesses stored in Pinnacle servers, the only thing they needed were bodies and Esora gave them robots.
Abyssmare is also transferred to Hope's Pinnacle. They were supposed to be some of the first students of the overseas campus until the Tragedy turned the overseas campus into the Future Foundation. Ibuki left the FF in the hands of Abyssmare while she went out trying to find all of her missing unit mates.
In her absence, the FF nearly fell apart as Abyssmare's endless internal conflicts allowed a shady board of Hope's Peak representatives to slide in and steal power away from them. That led to the final Killing Game Makoto went through, but once it was over, he was able to rescue Abyssmare and bring them to Japan to help fight the Tragedy there. Now, they are studying how to be proper Ultimate students from their Japanese classmates until the day finally arrives for them to return home to America, when the overseas campus is finally, officially finished. Unichord, meanwhile, is finally old enough to attend Hope's Pinnacle, having been in the middle school division for most of the DR storyline.