In the 31st century, Brainiac 5 and Bouncing Boy take refuge in Legion Headquarters and plan against an opponent who has defeated every Legion member except the two of them. Brainiac 5 reveals he plans to use a Time Bubble to recruit heroes from the past, despite the risk to history. According to the historical records, three members of the Justice League traveled to the future, and now is the time. Bouncing Boy notes that only two of them ever made it home.
Under Green Lantern's watchful eye, Supergirl goes into battle against two super villains. It turns out they're in a holographic simulation. When she says it isn't much of a fighter, Green Arrow and Superman, monitoring the training exercise, send in simulations of Blockbuster and Atomic Skull. As she fights, Green Arrow notes to Superman that his cousin is more interested in training then celebrating her 21st birthday. He points out that Superman doesn't spend time with Supergirl, who grew up in a highly advanced civilization before coming to Earth. Superman insists he's stepped back to let her develop on her own, but Green Arrow says she could use some family support.
Kara completes the training exercise and Green Lantern admits she's learned everything he has to teach her. Green Arrow enters the simulation just as sphere appears around them, causing them to disappear before Superman can do anything. In the 31st century, Supergirl mistakes Brainiac 5 for his ancestor and attacks him. He protects himself with a force field long enough for Green Arrow to call Supergirl off so Brainiac 5 can explain he's a biological descendent of the 21st century artificial intelligence. The Legionnaires explain they're in the 31st century and introduce themselves. Brainiac 5 then explains that a team of villains the Fatal Five, attacked the Legion and captured most of its members. As the Leaguers privately talk, Bouncing Boy warns Brainiac 5 that they took Supergirl from the day she's destined to die.
The Leaguers agree to help but glowing Emerald Eye appears: an artifact belonging to the Emerald Empress. She and her teammate, the Persuader, attack. The Empress subdues Green Arrow and attaches a mind-control disk to his forehead. The Persuader overwhelms Green Lantern and Bouncing Boy, and attached mind control disks to Bouncing Boy as well. When Brainiac 5 goes after the Empress, she attaches a disk to him but he resists it. Green Lantern and Supergirl are defeated and mind controlled as well, but Brainiac 5 removes Supergirl's disk. The Persuader blasts them, knocking Green Arrow aside as well. Emerald Empress orders a retreat now that they have Green Lantern, and the villains depart.
After freeing Green Arrow, Brainiac analyzes the mind control device and tries to track it to the source, but the Fatal Five are masking the carrier way. Supergirl wonders why Brainiac 5 freed her first, and Green Arrow points out that John Stewart was more powerful. Brainiac 5 is forced to admit he's fallen in love with Supergirl, and Green Arrow leaves them alone.
In hyperspace, Tharok, a half-man/half-machine cyborg, wonders why Emerald Empress and Persuader failed. He warns them that wasn't part of the plan, but Emerald Empress insists they are more powerful than ever.
On Earth, Brainiac 5 tries to track the captured Legionnaires by their flight rings without success. Supergirl realizes they can track Green Lantern by his League communicator. Green Arrow finishes upgrading his arrows with futuristic technology as Brainiac 5 determines the Fatal Five are heading for the capital of the United Planets. Brainiac 5 goes after them in his personal cruiser. They arrive in orbit to find the Fatal Five's ship... and a team of mind controlled Legionnaires descending to attack the planet, accompanied by Green Lantern.
Supergirl goes to hold off John and the Legion, while Brainiac 5 and Green Arrow infiltrate the Fatal Five's ship. Brainiac 5 admits he likes her and doesn't want her to go, and finally explains her destiny not to return from the battle. Supergirl insists on going to defend the capital, then kisses him before leaving. Brainiac 5 takes his cruiser on an attack run and smashes through the hull.
Supergirl confronts the mind-controlled heroes on the planet below. On the Fatal Five's ship, Green Arrow and Brainiac 5 burst into the bridge only to find the five villains together. They manage to hold the villains off long enough for Green Arrow to take out the ship's controls.
On the planet below, Green Lantern leads the final assault and prepares to kill Supergirl... just as the mind control is freed. Green Lantern holds Supergirl in his arms. On the ship, the two heroes are overwhelmed, but Green Lantern, a recovered Supergirl, and the Legion arrive just in time to rescue them.
Later, the Legion makes the League members honorary Legionnaires and bid them farewell. Supergirl looks at Brainiac 5 and then says that she plans to stay and join the Legion of Super Heroes. Her choice assures that history remains the same, since she never returned to the present from the mission.
Aboard the Watchtower, Superman and Steel attempt to get a fix on the missing members when Green Arrow and Green Lantern appear. They give Superman a cube: a going away message from Supergirl, saying she loves him and she wants to stay in the future where she can be more than just "Superman's cousin," and she has a boy. Superman accepts her judgement but worries that he didn't tell Kara he loved her. Green Arrow assures him that she knows. Now all they have to do is explain to Superman that his cousin is dating a Brainiac...