As Atom is being introduced into the Justice League, they receive word that Joker is invading Metropolis with the intent of poisoning the city with his Joker gas and remodeling the Daily Planet. As the Justice League arrive at Metropolis, they notice the absence of The Flash, much to Batman's chagrin. Meanwhile Flash is busy getting snacks across the country and catching criminals (including stopping Captain Cold from robbing a bank and stopping Captain Boomerang in a car chase) along the way and is horrified when he discovers he missed the trouble alert. By the time he arrives at Metropolis, although The Atom was able to create an antidote for the Joker Gas, Joker succeeded in redecorating the Daily Planet with his "Fun Cannon" (though Flash is able to undo this). The Justice League is upset with Flash's impulsive decisions and state that he needs to slow down and put more thought into his actions. Right at that moment, a yellow, vibrating speedster taunts Flash for his inferior speed and a chase ensues that ends with Flash waking up in his bed the next day. After realizing how similar the events to this day are to the previous, Flash realizes he had been sent back to the morning of that day and thus is able to prevent Joker from firing his Fun Cannon. But the yellow speedster returns and taunts Flash again which results in Flash repeatedly having to chase the speedster in the form of a time loop and prevent the various crimes that occurred on that day. When Batman realizes that Flash is in a time loop he gives him advice on how to stop it, but once again the yellow speedster returns and gives Flash the chase. Following the speedster into a dimensional gateway, Flash has had enough of his taunts and pushes his own power past its maximum which results in him overtaking the speedster and breaking the loop, but at a cost.
Flash returns to Central City having unknowingly been sent five days into the future and to his surprise, the city has turned against him, his powers are gone and he has been framed for various pranks pulled on the Justice League (to the point where Batman revokes his membership). Crestfallen and de-powered, Flash ponders about what to do now. At that moment, the speedster that continuously taunted him (and the true perpetrator of the pranks on the Justice League) reveals himself as the Reverse Flash, a speedster from the future who grew envious of Flash's fame in the past and traveled back in time to steal Flash's fame and purpose and plans to do the same to the rest of the Justice League. Atom, having shrunk down and followed Flash home overhears everything, but as Reverse Flash rushes off and restrains Flash, his suit short circuits, preventing him from returning to his normal size. Fortunately, Atom manages to free Flash and phone Doctor Fate in order to help the Flash regain his powers. While Flash is teleported to Doctor Fate's residence, Atom attempts to return to the Hall of Justice to reveal Reverse Flash's plan to his fellow Leaguers, which at his small size is much easier said than done. Meanwhile Reverse Flash is able to prevent crime and commit acts of heroism at a rate quicker than the Justice League can get to them. This allows Reverse Flash to gain the popularity of the public and render the Justice League obsolete.
Elsewhere, Flash finds himself at Doctor Fate's tower and is introduced to Doctor Fate and his assistant Zatanna. After Flash explains his predicament to Doctor Fate, Doctor Fate reveals that by overloading his powers, he broke his connection to the Speed Force which he proceeds to explain to the Flash. Doctor Fate and Zatanna then proceed to send Flash into the Speed Force where Flash will be placed with various trials in order to prove his worthiness of his powers. Remembering the advice of his fellow Justice Leaguers, Flash is able to complete the trials and is introduced to the Speed Force Nexus, the primary source of power in the Speed Force. Right at that moment, Reverse Flash arrives and reveals that he planned for Flash to complete the trials so that he could acquire the Nexus without having to deal with the trials himself. As Reverse Flash steals the Nexus and places it into his suit, his powers become increased exponentially and he is able to leave Flash trapped in the Speed Force.
As the Justice League face retiring, Reverse Flash arrives and using the power of the Speed Force Nexus, he is able to encase the Hall of Justice in an oversized statue of himself which is made of bricks from the Speed Force impervious to their powers. Atom is able to arrive at the Hall of Justice just as the statue is completed, and with the help of Ace the Bathound, Krypto the Superdog and the Green Lantern B'dg, he is able to repair his suit (returning him to his normal size), help the Justice League fend off the security robots Reverse Flash reprogrammed, and help the Justice League escape to the Batcave. Flash also manages to return from the Speed Force by creating a vehicle out of the same material as Reverse Flash's statue.
Believing himself to have rightfully defeated the Justice League, Reverse Flash builds more statues of himself around multiple international landmarks and declares himself the ruler of Earth, threatening that those who disobey him will meet the same fate as the Justice League. However, to his surprise the Justice League arrive to defeat him, and using the bricks Flash brought with him from the Speed Force, they are able to rival Reverse Flash's speed and destroy his statues (thus sending the bricks he used to build them back to the Speed Force) before he can prevent this, allowing Flash to steal the Speed Force Nexus from him, which causes him to not only regain his powers, but also acquire greater speed than Reverse Flash. Flash then proceeds to taunt Reverse Flash much like he did during the time loop, prompting Reverse Flash to exceed the use of his own powers, resulting in him returning to the Hall of Justice de-powered and arrested by the Justice League. With his powers restored, Flash takes Reverse Flash to prison and returns the Nexus to the Speed Force in order to avoid its power from ever falling into the wrong hands again. After that, Flash is reinstated into the Justice League. Batman then reveals that he was fully aware of the time loop and the fact that Reverse Flash was responsible for the pranks pulled on the Justice League and fired Flash so that Atom could spy on him to prove him right and notify Doctor Fate. Flash is grateful for the restoration of his powers and the advice the Justice League gave him and the Justice League celebrate their victory as Doctor Fate overlooks everything.
- Dee Bradley Baker as Captain Boomerang, Aquaman
- Troy Baker as Batman
- Eric Bauza as Atom, B'dg, Jimmy Olsen
- Grey Griffin as Wonder Woman, Lois Lane
- Tom Kenny as Plastic Man, The Penguin
- Phil LaMarr as Firestorm
- Vanessa Marshall as Poison Ivy
- Kate Micucci as Zatanna
- Nolan North as Superman, Killer Croc
- Khary Payton as Cyborg
- Kevin Michael Richardson as Doctor Fate, Captain Cold
- Dwight Schultz as Reverse Flash
- Jason Spisak as The Joker
- James Arnold Taylor as The Flash
- Audrey Wasilewski as Mayor Wimbley
- Grey Griffin reprises her roles from LEGO DC Comics: Batman Be-Leaguered. She also voiced Naare in LEGO Star Wars: The Freemaker Adventures.
- James Arnold Taylor reprises his role as The Flash, and is known for voicing Obi-Wan Kenobi in Star Wars: The Clone Wars.
- This is the first movie not to focus on Batman
- This is the first LEGO DC Movie that does not come with a minifigure