Prime and Luthor went to Metropolis where all the supervillains on Earth were trying to wreck the city, and the heroes showed up and beat the snot out of them. Prime got really angry and ran off to Oa because he think he can restart the universe by flying through the core of Oa at lightspeed (How exaclty this would restart the universe, I have NO idea)...
Anyway, the Green Lantern Corps comes together to stop him with a solid wall of ring energy and then a spider's web once Prime breaks that down, and this gives Superman and Kal-L enough time to catch up. So they fly him through Krypton's sun, stripping them all of their powers. Prime fatally wails on Kal-L and then Kal-El defeats Superboy-Prime. Kal-L dies in Power Girl's arms.
Later, Bats, Supes, and Wonder Woman all decide to take the year off. Superman doesn't really have a choice. Luthor tracks down Alexander and has the Joker kill him, then we see on Oa Superboy-Prime his trapped in a Green Lantern prison under a Red Sun and carves the Superman symbol into his chest. THen he swears he'll get out and starts drooling. The end.