In Tokyo, the citizens run in panic from a giant flying fire-breathing turtle. S.T.R.I.P.E. and Stargirl try to get it out into the harbor but Stargirl attacks prematurely despite S.T.R.I.P.E.'s warning. It fires a blast of flames at it, knocking her back, and S.T.R.I.P.E. calls in Green Lantern. S.T.R.I.P.E. launches an attack to stall it and the monster takes to the air and comes after the heroes. They lure it out to a tanker in the harbor but Stargirl attacks prematurely, dropping it onto the tanker. Supergirl arrives and the gas canisters on the tanker go off, causing the monster to shrink to normal turtle size. The crowd cheer but Stargirl discovers that all of the teenage girls are Supergirl fans from the local Supergirl convention. Green Lantern is unhappy about Stargirl grandstanding but Stargirl is unhappy with being upstaged.
The team flies back to the U.S. passing over the Arctic, with Supergirl flying while Stargirl complains from the passenger compartment. Suddenly the Javelin is enveloped in mystical energies and pulled toward a rift in the ice. The Javelin descends down a tunnel below and passes out into a vast underground kingdom. The back half of the Javelin is ripped free and the ship comes in for a crash landing. They're unable to contact the Watchtower and discover that there's a sun in the sky and no signs of an exit. Several lizard soldiers riding dinosaurs arrive and advance on them, firing advanced energy weapons. Supergirl goes after them only to discover that her powers are only working at half strength. The others fend off the attackers, who retreat. However, pterodactyl warriors arrive Green Lantern holds them off while ordering Stargirl to protect Supergirl. Stargirl eventually gets around to helping her while Green Lantern and S.T.R.I.P.E. defeat the rest. A Tyrannosaurus Rex attacks, but is shot down by... Travis Morgan, who introduces himself as Warlord of Shamballah.
Warlord takes them to his village/fortress of Skataris and provides them with a feast, and his daughter Jennifer explains that they needed help and used her magic to summon them. Warlord shows them his people, who are practicing to defend themselves against their enemy Deimos. Supergirl promises they'll do whatever they can to help and Warlord explains that Deimos is an evil wizard who has recently pushed to start conquering Shamballah and equipped his dinotroopers with energy weapons. Warlord explains he came through the portal and made himself at home. His new people are trapped between Deimos and the "Great Stone," the latter kept in a tabernacle inside a mountain. Deimos plans to get the Great Stone.
At Deimos' camp, a dinotrooper reports that the newcomers escaped. The dinotrooper draws Supergirl's symbol and Deimos destroys his minion for its failure. The wizard then turns to his military advisors: Metallo and Silver Banshee.
The League members and Warlord go to the tabernacle where the latter's friend Machiste is waiting for them. Machiste explains that he was healed by the Great Stone, but warns that it can kill or cure. The monks open the temple to the chamber, revealing that it's an enormous piece of kryptonite. Supergirl collapses and they hastily seal the door. A werepanther, Shakira, arrives and warns them that Deimos is there. They go to the walls to see a vast army of dinotroops advancing on Skataris. Warlord commands his people to attack and the League lends their abilities to the battle. Supergirl insists on fighting despite her reduced powers and against Green Lantern's orders. Giant serpents attack and Jennifer summons a flamebird to destroy them. However, Warlord's forces discover their enemies have a new ally: Silver Banshee. Green Lantern gags her with his power ring but releases her when he comes under attack. By the time he can turn back, she's escaped the battlefield.
Deimos' troops fire robot drills that create a tunnel to the tabernacle. Deimos enters and tells Metallo to take the Great Stone, but Stargirl attacks him. The wizard attacks her using wrist blasters but she uses her Star Staff to destroy them. However, Metallo captures her from behind. Warlord arrives and challenges Deimos, who accepts. As the two men battle, Stargirl flies up into the air and smashes Metallo into the ceiling. Unaffected, he knocks her unconscious and advances upon the Great Stone. Supergirl arrives and warns him to stop. He fires a kryptonite blast at her and she dodges and grabs the Star Staff. She smashes it into his shoulder, penetrating his armor and forcing him to discard the robot limb. She runs outside and he chases after her, and she topples a statue on top of him.
As Deimos and Warlord fight their way up the mountain stairs, Metallo frees himself and goes after Supergirl. Supergirl stays one step ahead of her opponent, while Warlord disarms Deimos. The wizard warns that Warlord will never unite the lands but Warlord refuses to hear it. Deimos lunges after him and goes over the stairs, falling into the abyss below.
Supergirl gets to the battlefield and takes a blaster, then tries to shoot Metallo without success. He moves after her as she climbs the stairs to the top of the wall but he scores a hit with a kryptonite beam. He grabs her but she lets him pull her close enough to use a dagger and cut out his kryptonite power core. The exposed radiation is killing Supergirl... until Stargirl arrives to dispose of it.
Warlord and his people celebrate their triumph and their new freedom. Green Lantern questions Metallo why he needs so much kryptonite. When Metallo refuses to talk, Green Lantern notes that his systems will soon shut down for good. Metallo starts to explain who he's working with but his systems self-destruct and Green Lantern realizes it isn't Silver Banshee's work. Warlord checks with them and they say that the Great Stone should stay there will it do some good. Green Lantern agrees but only if they seal the portal for good. The heroes head back to the surface and close off the portal, and Supergirl flies off. Stargirl goes in pursuit and the two of them compare notes on their overly protective guardians. Green Lantern takes Metallo in tow so that J'onn can scan him, and the heroes wonder what is going on.