The history of Jonathan Storm of Earth-9997 mirrors that of his Earth-616 counterpart. In modern times he remained a member of the Fantastic Four. Johnny was with the team when they were dispatched along with Captain America to stop Namor and Dr. Doom from attacking the United Nations. During the battle, Johnny attacked Namor, who had been manipulated by Doom once more.
In the insuing battle, Johnny's neck was broken by Namor and he was killed instantly, his nephew Franklin would curse Namor to burn for the rest of his life. Johnny's soul would end up in the Realm of the Dead, where it would be recruited by Mar-Vel in his quest to defeat Death. Before initiating his quest, which included collecting items of power on Earth, Mar-Vel would convince Johnny that he was dead (as all those dwelling in the Realm believed themselves to be alive, and those who were still alive were those who were deceased) in order to help in resurrecting Susan Richards for Reed Richards.
Johnny, would convince his sister that she is dead by having convincing Dr. Doom to apologize to her for all the misery he caused her family.
Following Sue's resurrection, Johnny would aid Mar-Vel in his battle against Death. Later following the death of Death, Johnny would be admitted into Paradise where he would be given a shard of the Cosmic Cube to create his own ideal paradise. Johnny would live a life of a celebrity race car driver, however the reality in which he lived as a success, Johnny soon grew bored and devolved into a bout of alcoholism and excesses. He was one of the few in Paradise who was not pulled out of their personal paradise to help in the counter attack against the Kree invasion of Paradise. Johnny would later be shaken out of his stupor and released from his paradise by Reed Richards, who took over the Cosmic Conciousness from Mar-Vel. Johnny's current fate following the liberation of Paradise remains unrevealed.