The Superman (and Lois Lane) of Earth-Two, Superboy of Earth-Prime, and Alexander Luthor, Jr. of Earth-Three, from their home in the hidden pocket universe, were revealed to be observing the events of the newly formed universe as well as the actions of its heroes. Upon observing the events leading up to Infinite Crisis, the heroes returned to the universe in an attempt to restore Earth-Two's existence, at the expense of Earth-One.
The Anti-Monitor's remains were then used as part of a tuning fork, similar to the ones used during the first Crisis. This construct then created the vibrational frequency that Earth-Two was on prior to its nonexistence, which in turn recreated Earth-Two with no visible expense to Earth-One, save the movement of characters who originated on Earth-Two to the recreated Earth-Two. Alexander Luthor then recreated the other Earths with his tuning fork, with their respective heroes forcibly migrating to said Earths. Superboy-Prime (followed soon by Bart Allen) then returned from the Speed Force wearing what appeared to be select elements of the Anti-Monitor's armor, using it as a yellow sunlight collector. Ultimately, the tower was destroyed when Kon-El, the modern Superboy, and Superboy-Prime crashed into it while fighting each other; Kon-El died in the arms of Wonder Girl as Superboy-Prime fled.