After taking over the villains, Lex Luthor is considering the piece of Brainiac he has storage unit, and Tala tries to comfort him. Lex continues with his experiment but is unable to reconstitute Brainiac. Grodd is captured, and Luthor demands answers from him – Grodd doesn't cooperate. Tala advises Lex to use her magic to access Grodd's knowledge and gain the information.
The villains confront Lex to challenge his leadership and he responds by saying he can get them money. At the Watchtower, Mr. Terrific suggests that Dr. Fate mystically trace the resonance from Grodd's previous takeover of the Flash. At the same time Luthor types into Grodd's mind through his technology, tying his brain into Grodd's. There's a burst of energy and both Lex and Flash collapse. Fate realizes it's Luthor's mind in Flash's body – he superspeeds to the teleporter and makes a run for it, escaping. They also realize where Flash is…in Luthor's body.
Flash-in-Lex quickly recovers while aboard the Watchtower, Mr. Terrific puts out the alert. Lex-in-Flash has taken out many of the Leaguers but Fate and Green Lantern go to intercept him. They find his tracking unit and go to check the other escape routes while Dr. Fate meditates to analyze the mind-switch. Tala advises Flash-in-Lex against the other villains who are conspiring against him, and Flash-in-Lex is unable to make outside contact.
Lex-in-Flash manages to get to a Javelin and rams his way out through the bay doors. Red Tornado pits his whirlwind against the Flash's while Flash-in-Lex tries to give a speech to the villains. He gets them to recap their plan against Kasnia, robbing its treasury. Lex-in-Flash unmasks himself…but has no idea who Wally West is. Flash-in-Lex has no choice but to go forward with Lex's plan when Grodd asks to meet him, and reveals he knows about the mind-transfer.
Grodd refuses to negotiate and decides to wait until Flash-in-Lex's ruse is discovered. Fate has figured out a way to reverse the spell and goes to the Flash, who is cornered in the cafeteria. Fate manages to restrain him but is then stunned and Lex-in-Flash makes another run for it.
The villains close on the Kasnian money shipment and Sinestro and Dr. Polaris attack. Sinestro reroutes the train to a nearby cave and Tala teleports out the money. Lex-in-Flash contacts the villains and informs them of the switch, who capture him. Mr. Terrific sends a team to the coordinates while Green Lantern is decoyed while the Flash goes to the bridge and then rebuilds the primary transporter. Dr. Light, Steel, and Ice arrive in Kasnia and track the train to the cave to battle Tala, Dr. Polaris, and Sinestro. The villains are forced to retreat through a magical portal, leaving the money behind.
Mr. Terrific turns off the Watchtower's gravity, lifting the Flash into the air long enough to bring him back down…hard. Dr. Fate casts a spell and Flash is restored to his original body. Flash doesn't have anything to reveal about the headquarters except that it's in a swamp. The other villains beat up on the real Lex, and Polaris takes over the villains. Lex activates a belt control reversing Dr. Polaris' polarity, demonstrating he is who he says.