The Joker kills him with slight help from Lex Luthor.

Just prior to Earth 3 being destroyed by a wave of anti matter unleashed by the Anti monitor, Earth 3's Alexander Luthor placed his infant son Alex into a dimensional top and sent him hurtling through the universes to Earth 1.

The top spun through the anti matter wave, imbuing the child with both positive and anti matter energy, making young Alex a living matter transformer. Arriving on Earth 1, Alex was brought aboard a sattelite belonging to the Monitor, where Alex quickly changed from infant to child to teenager.

There, Alex discovered his powers. Able to summon his anti matter abillities, the youth could bridge universes from positive matter to anti matter, and he could use himself to let other positive matter beings enter the anti matter universe without harm.

At the end of the Crisis on Infinite Earths, Alexander Luthor opened a one-way portal to an unknown dimension, which allowed the Superman of Earth -2, his wife Lois Lane and Superboy of Earth Prime to be saved, along with himself, surving the annihilation of the Anti monitor. The recent Infinite Crisis has seen a number of those characters return to the mainstream of the DCU as the Multiverse appears to have returned.