In the early 1940s; with Nazi Germany invading most of Europe, and Adolf Hitler after magical artifacts, Franklin D. Roosevelt is asked by Colonel Steve Trevor to finally get Americans involved, by creating a team of superhumans. Consisting of Black Canary, Hawkman, Hourman, Flash, Trevor and led by Wonder Woman, the Justice Society of America is given the go.
In the present day, Barry Allen and Iris West have a picnic in Metropolis hoping to get away from "work". However, their picnic is disrupted by Superman fighting Brainiac, and Flash comes to Superman's aid. When Brainiac fires a Kryptonite bullet, Flash goes so fast trying to catch it that he channels the Speed Force for the first time.
Led by the voice of Doctor Fate, he arrives in the past during a battle between the JSA and the Nazis in France. Despite the confusion over his allegiance, the team realizes Barry is an ally when he defeats a group of Nazis and saves Trevor, and believe that he is from the future. While the team deploys to stop a second attack wave, Barry takes Trevor back to base, where he learns about the JSA, a secret superhero team he never heard of until now.
After meeting "Shakespeare", the JSA war correspondent - who looks vaguely familiar to Barry - and Trevor making a pass at proposing to Diana, the team meets up for their next mission. Despite the risk of causing a time paradox, the heroes realize that need Barry's help in saving a codebreaker from a Nazi fortress who can decode a message Trevor stole.
Arriving at the fortress, the heroes, Trevor and "Shakespeare" break in, defeat the guards, and discover several prisoners in the dungeons. "Shakespeare" rescues one prisoner who tells that someone told him of "Shakepeare's" arrival, gives him a package with a red and blue suit inside, and implores him to prevent something from happening. A guard attacks "Shakespeare", only for the bullets to bounce off him. Diana, Barry, and Trevor arrive. "Shakespeare" identifies himself as Clark Kent. But when Clark reveals a background different from the Clark he knows, Barry realizes that he is not in the past, but in a parallel reality. The rest of the team finds the codebreaker, whom Hawkman recognizes as Doctor Fate. Breaking the code with his powers, Fate directs the team to the Bermuda Triangle before he disappears.
Arriving at the Bermuda Triangle by sub, the team is detected by Nazi warships. After depth charges disable the engines, the two Flashes jump-start the sub just while Diana torpedoes out to destroy the enemy ships. The heroes are saved by the soldiers of Atlantis, who direct them to an outpost underneath the Bermuda Triangle. Met by The Advisor, the team meets Aquaman who traps them in a prison. It is revealed that Aquaman is under the control of The Advisor, who is influencing the Atlanteans to work with the Nazis and afterwards plans to take over the planet once Atlantis has destroyed the Nazis. The two Flashes realize they both are becoming weaker when they are together, so they work together to regain their strength and break out of the prison. The team splits up: One heading for New York, which the Atlanteans and Nazis are targeting, while Barry and Diana try - and fail - to stop Aquaman and The Advisor from releasing monsters from The Trench.
Atlantis begins its invasion in Manhattan, attacking everybody until the JSA arrives. They gain the upper hand until the Trench monsters arrive. Hawkman is killed and Hourman is wounded. Jay and Canary destroy the monsters, while Diana and Barry arrive and fight Aquaman. Diana destroys Aquaman's trident, bringing him back to his senses. When he comes to and sees what he has done, Aquaman retreats in shame, ending the battle. The Advisor reappears and reveals that a follow-up strike by Nazi bombers is following; he fatally stabs Trevor with the broken trident before Barry knocks him out. Hope seems lost until Clark, clad in his Superman costume, arrives and destroys the bomber fleet. Diana and Trevor say their goodbyes as Trevor passes away.
Barry realizes he must go back to his Earth. He and the JSA say their goodbyes with Diana handing over the ring Trevor gave her, telling Flash not to make the same mistake about missed opportunities with his loved ones. Jay and Barry superspeed together and send Barry back to the very moment where he intercepts the Kryptonite bullet. After destroying Brainiac with it, Barry makes a proposal to Superman: With more enemies and heroes emerging, he suggests they form a team. Barry meets back up with Iris and decides to propose to her which she accepts.
