The first scene of this story is set in the future. The Legion of Superheroes is trying to save civilians from disappearing into nothingness: the future is disappearing, and according to Brainiac 5, it's all because of his ancestor, Brainiac 1. Brainiac 5 has established that his ancestor had killed Superman, which has resulted in the capture of all bottled cities. Since all the planets of the 31st century are originary from those bottled cities, and the cities were never released, then the planets never could have existed. As Brainiac borrows energy from fellow legionnaires, he disappears back to the present promising to see them again and saying: "Long Live the Legion".
In the present, Brainiac has started to invade New Krypton. As the Legion of Superheroes' Espionnage Squad recruit Mon-El and Superboy to help them save the bottled cities, Supergirl and Alura battle on New Krypton.
Once they are all reunited, General Zod asks Supergirl and Mon-El to leave before orderring his troops to arrest the Legion.
Alura comes in to prevent them from escaping, and fights Superboy. Supergirl arrives and sees her "cousin" hurting her mother. As they tell her Zod orderred their arrest, Supergirl explains to Alura the Legion is a Superhero team.
Alura goes and meets General Zod for more informition on his battle technique while the Legion attacks Brainiac's ship to free the bottled cities.
Thanks to Brainiac 5, they manage to breach the security field. Superman and Mon-El have managed to save one bottled city. Outside, New Krypton is invaded and Kandor is turned into another bottled city.
As Superman tries to save Kandor, he is hit with a blast of red sunlight, and falls in the middle of the sky.
It is then revealed that Brainiac 1 worked alongside Lex Luthor and General Zod to destroy New Krypton...