Issue 1 starts, with the exception of what may be a flash-forward, straight from the scene in Final Crisis #3 (Page 13) where Clark Kent sits beside Lois Lane’s hospital bed.
Zillo Valla, one of the Monitors, approaches Kent and tells him she is aware of his being Superman and offers him a chance to save his dying wife if he will accompany her in a race to save time. She uses her powers to take them to her ship which is apparently being flown by various superheroes from alternate universes, among them are Overman a German Superman, a Captain Marvel and a Captain Adam who appears to be the character Nix Uotan drew on Page 9 – Panel 5 of Final Crisis #2.
Valla’s ship, the “Ultima Thule”, is under attack by the destroyer “Echo of Midnight” which in turn is being attacked by Ultraman of the Anti-Matter Earth. The battle between ships takes Valla’s ship through universes, prompting Superman to help stall the destroyer until they reach Earth-51 which was destroyed at the end of Countdown To Final Crisis. The destroyer crash lands on Earth-51 while the “Ultima Thule” runs aground on “the shores of oblivion”; on board the various super heroes argue about what Valla has promised them, with Ultraman threatening the others.
The heroes disembark and are greeted by Merryman, the King of Limbo. Readers of Grant Morrison’s run on Animal Man will recognise both the character and the setting which Merryman calls Limbo. The heroes attempt to find help in Limbo to repair the “Ultima Thule” and find the one book in the Library of Limbo. If it can be taken back to the “Ultima Thule” it can be used to repair the ship.
Trying to lift it, Superman and Captain Marvel have revealed to them the origin of the Monitors before causing an explosion that returns Captain Marvel to his alter ego of Billy Batson. Superman takes Batson back to the ship, planning to return for the book. Instead he finds Valla feeding on Overman and apparently revelling in the fact that Mandrakk, the Dark Monitor has risen. Called outside by Captain Adam, Superman finds Ultraman holding the book from the Library, claiming that evil has triumped.
In the sky above him, the destroyer “Echo of Midnight” has found them.
Issue 2 begins with Overman proclaiming the ascendancy of Mandrakk which, to Superman, is simply a challenge. Around them, Merryman rallies his people.
In the Ultima Thule, Zillo Valla is saved from Overman’s revenge by Billy Batson who realises her vampiric attack on the German Superman was simply a way of restarting the Ultima Thule which runs on life’s blood. As a show of gratitude, she restores his magic word to him.
Outside, Merryman’s forces attack the army of Mandrakk as Ultraman attempts to start a fight with Superman again, once more prevented from doing so by the returned Captain Marvel. Superman charges Marvel with using the Ultima Thule to travel the multiverse and warn them of Mandrakk’s coming.
Captain Adam uses Superman and Ultraman’s clashing energies to power the ultimate weapon created by the first monitor and revealed in the book in the Library of Limbo: a huge thought-robot in the world of the Monitors. Powered by Superman, the robot faces the reborn Mandrakk in a clash of archetypes. During the battle Zillo Valla dies and civilisation falls until Superman finally overcomes him.
As the giant thought-robot succumbs to its injuries, it carves its epitaph on the gravestone Mandrakk had prepared for it before the thought forms of Superman and Ultraman return to the battle between the Ultima Thule and the Echo of Midnight. There the Superman of multiple worlds attack, destroying Mandrakk’s ship.
Ultraman is found by Ogama, the Monitor who plotted Nix Uotan’s exile and was a disciple of Mandrakk. He turns Ultraman into his willing pawn while elsewhere, Mandrakk plans his own return.
Back on Earth, Superman finds a healed Lois who tells him of a dream she had where she saw a tombstone engraved with the words “To be continued”