November 11th, 2024

In the present day, Johnny and his Legion of Doom try to use cryogenic rays from orbital satellites to expand the Earth's polar ice caps which will reduce sea levels and create new islands that they intend to rule. Ultraman and the Justice League confront the Legion, ultimately destroying the satellites. Refusing to accept defeat, Loki Loud overloads the remaining satellite which falls to Earth and freezes Johnny who is believed to be dead. In the future of the 31st century, teenage superheroes-in-training Dawnstar and Kitty Bobo are visiting a museum dedicated to the League's exploits. They accidentally release Johnny who has been in suspended animation for nearly a millennium following his battle with the League, and was relocated to the museum after being discovered and excavated in the 29th century. Johnny explores the museum, discovers Ultraman’s secret identity and locates an ancient item called the Eternity Glass which can manipulate time and space. Taking Loki’s weapon he freezes Dawnstar and Kitty. He then uses the Eternity Glass to release Time Trapper as his servant which allows him to travel to the point when he last fought the League, the young heroes then break free and follow the villain. Resuming control of the Legion, Johnny then instructs Time Trapper to send his forces back in time to prevent Jon and Martha Dent from adopting Kal-El in Smallville. The young heroes enlist the League to stop them and travel to the Hall of Justice in Washington D.C. After a misunderstanding the heroic duo explains their story and verify it through Faith’s Lasso of Truth. SpongeBob, McGee and AJ travel into the past to prevent Bizzaro, Toyman, Tigera and Dirge from sending Kal-El back into space while Ultraman and the rest of the League attempt to stall Johnny’s Legion in the present.

Despite the League's efforts the Legion sends Kal-El's ship away from Earth which creates a temporal paradox that erases the present League. In the League's absence the Legion pillages the world and leaves Washington D.C. in ruins. Unwilling to risk being erased from existence Dawnstar and Kitty Bobo retreat and as they do so the heroic duo realizes that they can induce their own paradox by ensuring that Johnny never obtained the Eternity Glass. They free Johnny’s past self from the ice but Time Trapper is immune to the paradox because he exists outside of time and with Johnny freed he can now do as he pleases because he is no longer the villain’s master. The Time Trapper banishes the future Johnny from existence and tries to remake the current world in his image. Ultraman and the League, who exist again because of the latter's absence, confront the villain. Time Trapper is too powerful for the League to fight. Kitty Bobo discovers that Time Trapper is composed entirely of dark matter and he also realizes that only Dawnstar's light-based powers can defeat him. Dawnstar charges Time Trapper and the League defeat him, reverting the Eternity Glass, which imprisons Time Trapper once more. The League thanks the young heroes and offers them the opportunity to stay but they refuse and return to their own time. Johnny is sent to Blackgate Prison after which Skips assumes control of the Legion of Doom. Returning to their own time Kitty Bobo and Dawnstar discover that a statue of Johnny has replaced a statue of Ultraman. Believing they have altered history in some unforeseen fashion the heroic duo immediately returns to the 21st century to help the League once more.