In the 31st century, Mano, Tharok, and Matthew Yang King as The Persuader launch a bold assault on the Legion of Super-Heroes' headquarters to seize their time sphere. Elyes Gabel as Star Boy, Tara Strong as Saturn Girl, and Noel Fisher as Brainiac 5 rush to hold them back, but the onslaught proves overwhelming. Just as the villains activate the sphere, Star Boy lunges at them and is drawn into the device. He lands in the 21st century and triggers a trap Brainiac 5 programmed, sealing the villains inside a stasis field. The sphere ends up in Metropolis, while Star Boy crash-lands in Gotham City, discovering that his medicine — needed to stabilize his mind — was destroyed in the rough landing and does not exist in this era. Without his meds, his behavior grows increasingly erratic, and Batman, voiced by Kevin Conroy, apprehends him and sends him to Arkham Asylum. The stasis-locked time machine is eventually recovered by Superman, voiced by George Newbern, and brought to the Justice League's headquarters for analysis.
Ten months later, Diane Guerrero as Jessica Cruz / Green Lantern grapples with the trauma of a near-fatal encounter and the fear of leaving her apartment. Meanwhile, Susan Eisenberg as Wonder Woman continues to press for Jessica’s inclusion in the League, while Daniela Bobadilla as Miss Martian strives to prove herself to Batman for membership. A hostage situation at Gotham News Network (GNN), caused by Bloodsport, tests Miss Martian’s inexperience and resolve as she tries to navigate the crisis.
Back at the Watchtower, Kevin Michael Richardson as Mister Terrific accidentally deactivates the stasis field, freeing the trapped travelers. Superman clashes with the newly liberated foes, but is wounded by Persuader’s axe, allowing Emerald Empress and Validus to escape. The threat deepens as the Fatal Five move to strike again, their plan unfolding across city streets and skies alike.
Star Boy’s memory is jogged by a news report about the fight, and he breaks out of Arkham. The Justice League pieces together that they are dealing with time travelers, and Batman deduces that Jessica Cruz is their target. When the Five attack Jessica, Star Boy rushes to her aid, followed by Superman, Batman, Wonder Woman, Mister Terrific, and Miss Martian, who fight to keep the assailants from reaching the base. The encounter ends with the heroes forcing the Five into flight, and a wary but hopeful bond forms between Star Boy and Jessica.
Miss Martian uses her telepathic abilities to link herself, Batman, and Jessica with Star Boy’s mind, granting them a glimpse of the Legion’s past and the broader stakes involved. They witness a confrontation between the Legion and the Fatal Five, which resulted in Emerald Empress and Validus being captured and taken to Oa in the past. Upon awakening, the Justice League faces a stark ultimatum from Mano: surrender Jessica or face bombs across the United States. The first wave of attacks erupts in Metropolis, spurring the League to respond with precision and speed.
In the ensuing battles, Emerald Empress seizes the Green Lantern energy and reveals a master plan to devastate the Sun itself, wiping out humanity to prevent the Legion’s formation. Jessica, regaining her resolve, recites her oath and recharges her ring, returning to the fight with renewed purpose. She flies to reclaim the base and brings it down on the Fatal Five, ending their threat for good.
As Superman, Jessica, and Star Boy pursue the Eye, they are too late to stop it from plunging into the Sun. The star fractures, and Star Boy sacrifices himself by descending into the Sun’s core, using the full extent of his powers to repair it. The League honors his courage, and the Legion from the future arrives to pay tribute to their fallen comrade. In a final note of growth and inclusion, Batman informs Miss Martian that she has been invited to join the Justice League, and she accepts the offer, stepping into a larger role alongside her new teammates.