Superboy-Prime is drawn into the "Crisis on Infinite Earths" after his universe is consumed in the light of the Anti-Monitor. Although the loss of everything he knows causes him anguish, he finds peace in knowing that he fights the good fight alongside other heroes. During the final battle against the Anti-Monitor, Kal-L, the Earth-Two Superman, orders him to escape with Alexander Luthor, Jr. and the other heroes. Fearing that Kal-L will die in battle and knowing the new Earth is not his true home, Superboy-Prime joins Kal-L in the fight against the Anti-Monitor.